Multiple Animal Species Research Articles

The transcriptome of the parapoxvirus Orf virus reveals novel promoters for heterologous gene expression by poxvirus vectors

Orf virus (ORFV) has been used as a vaccine delivery vector for multiple animal species. Several strategies are being used to improve the immunogenicity and efficacy of ORFV vectors, including the use of poxviral promoter(s) with strong early and late activity capable of driving the expression of the heterologous genes for a prolonged time and eliciting a potent immune response. Here, we used RNA-sequencing (RNA-Seq) approach to analyze the transcriptome of ORFV during infection in primary ovine cells. Based on the transcriptional profile of individual ORFV genes, we identified ORFV promoters with strong early and late activity and have shown that they can be used to express heterologous genes in ORFV vectors. Our results show that the intergenic regulatory sequence containing core promoter sequences present upstream of ORF112 (p112) and ORF116 (p116) lead to markedly higher transgene expression than conventional poxviral promoters. Thus, these promoters are valuable alternatives to express transgenes in poxviral vectors.

Fusion of visible and thermal images improves automated detection and classification of animals for drone surveys

Visible and thermal images acquired from drones (unoccupied aircraft systems) have substantially improved animal monitoring. Combining complementary information from both image types provides a powerful approach for automating detection and classification of multiple animal species to augment drone surveys. We compared eight image fusion methods using thermal and visible drone images combined with two supervised deep learning models, to evaluate the detection and classification of white-tailed deer (Odocoileus virginianus), domestic cow (Bos taurus), and domestic horse (Equus caballus). We classified visible and thermal images separately and compared them with the results of image fusion. Fused images provided minimal improvement for cows and horses compared to visible images alone, likely because the size, shape, and color of these species made them conspicuous against the background. For white-tailed deer, which were typically cryptic against their backgrounds and often in shadows in visible images, the added information from thermal images improved detection and classification in fusion methods from 15 to 85%. Our results suggest that image fusion is ideal for surveying animals inconspicuous from their backgrounds, and our approach uses few image pairs to train compared to typical machine-learning methods. We discuss computational and field considerations to improve drone surveys using our fusion approach.

Whole-genome sequencing and phylogenetic analysis capture the emergence of a multi-drug resistant Salmonella enterica serovar Infantis clone from diagnostic animal samples in the United States.

Salmonella enterica is a major cause of foodborne illness in the United States. A multi-drug resistant (MDR) emergent Salmonella Infantis (ESI) with a megaplasmid (pESI) was first identified in Israel and Italy and subsequently reported worldwide. The ESI clone carrying an extended spectrum β-lactamase blaCTX-M-65 on a pESI-like plasmid and a mutation in the gyrA gene has recently been found in the United States in poultry meat. We analyzed the phenotypic and genotypic antimicrobial resistance, genomics and phylogeny of 200 S. infantis isolates from animal diagnostic samples. Of these, 33.5% were resistant to at least one antimicrobial and 19.5% were multi-drug resistant (MDR). Eleven isolates from different animal sources were phenotypically and genetically similar to the ESI clone. These isolates had a D87Y mutation in the gyrA gene conferring reduced susceptibility to ciprofloxacin and harbored a combination of 6-10 resistance genes: blaCTX-M-65, aac(3)-IVa, aadA1, aph(4)-Ia, aph(3')-Ia, floR, sul1, dfrA14, tetA, and fosA. These 11 isolates carried class I and class II integrons and three virulence genes: sinH, involved in adhesion and invasion, ybtQ and ybtP, associated with iron transport. These isolates were also closely related to each other (separated by 7 to 27 SNPs) and phylogenetically related to the ESI clone recently found in the U.S. This dataset captured the emergence of the MDR ESI clone in multiple animal species and the first report of a pESI-like plasmid in isolates from horses in the U.S.

Opioid-Induced Doctor Dolittle Phenomenon

AbstractBackgroundThe Doctor Dolittle delusion, of animals conversing with the sufferer, has not heretofore been reported to occur with heroin intoxication.MethodsThis 23-year-old right-handed single male used heroin daily since the age of 19. For 2 years prior to presentation, 1 hour after injecting at least one bag of heroin IV, he developed hallucinations of animals talking to him. The voices would occur simultaneously with moving their mouths. Dogs would bark, cats would meow, and birds would squawk his name. Insects would engage him in friendly conversation. Different pitches of voice were produced from each animal; birds were high-pitched; squirrels, insects, and cats were lower-pitched; dogs were medium-pitched. As his intoxication resolved, the hallucinations also evaporated.ResultsMental Status Examination: Oriented x 1, able to recall five digits forwards and three digits backwards. Able to remember none of four objects in 3 minutes without reinforcement and three with reinforcement. Able to spell the word “world” forwards but not backwards.DiscussionThe hallucination of animals talking, coincident with their mouths moving, articulating the words, associated with intoxication with high doses of heroin, with resolution with elimination of heroin, suggests opioid intoxication is the causative factor. The mechanism of zoopsia in Parkinson’s disease has been attributed to dysfunction of the inferior longitudinal and inferior fronto-occipital fasciculi which relay visual information from the occipital cortex to the temporal and the orbitofrontal cortices. Heroin may have induced cortical inhibition, disinhibiting such pathways and thus facilitating these hallucinations. The simultaneous congruent auditory and visual hallucinations suggests a central origin of these, controlling both the auditory and visual system, such as the left superior and middle temporal gyrus, or possibly the cerebellar vermis. What is unique about the current description is that multiple animal and insect species were involved, and that the pitch of their voice was species specific (high-pitched in birds, and low-pitched in rodents and insects). The pitch may reflect the individual’s personal hedonics towards the type of animal or the individual’s interpretations of mass media’s representation of these animals (i.e., cartoons of Looney Toons high-pitched Tweety Bird or Disney’s low-pitched Jiminy Cricket). While it is possibly due to the opioids themselves, heroin is frequently adulterated with fillers which may contain hallucinogenic properties, any of which may have been the pathogenic factor. Autophobia, or the need for social contact, may be the nidus motivating such communicative anthropomorphism. Query as to the presence of such Doctor Dolittle hallucinations in those with heroin or other intoxicants may be revealing.FundingNo Funding

Modelling growth in Suffolk and Charollais sheep populations using random regression models and validation of constrained polynomial correlation values

Random regression modelling has been used across multiple animal species to model longitudinal data. The random regression model for growth accounts for the genetic correlation between measures of the same trait over time and the wide environmental variability in growth, but this requires adequate weight records across the age range. However, contemporary management practices in sheep in the United Kingdom generally focus on growing lambs and neglect mature weight recordings. This study examined modelling strategies for growth data in Suffolk and Charollais sheep, provided by the Agriculture and Horticulture Development Board, with polynomial random regression modelling with many early life weight recordings but limited weight recordings in mature animals. Two methods were employed to model the data. In Method A, missing mature weight records were predicted for those animals that did not have a recorded mature weight. The animals were sorted into groups based on the identity of their sires and the year in which the animal was born. Mature weight values were predicted within each group with a multiple regression model. The dataset, including predicted values, was analysed with random regression models using polynomials and simple linear regression for animal and permanent environmental (PE) effects. In Method B, the dataset with missing mature weight records was analysed using a random linear regression animal model with random animal and PE effects. Due to problems of convergence because the parameters were close to the boundary space, fixing the correlation between the intercept and slope of the Legendre polynomial at different levels was investigated. The heritability values resulting from the model with a fixed correlation between intercept and slope parameters at 0.5 for the Suffolk dataset resulted in heritability values ranging from 0.2 to 0.5 from 1 to 619 days of age. Corresponding estimates for the Charollais dataset ranged from 0.18 to 0.49 from 1 to 640 days of age. For the Suffolk data, the genetic correlations ranged from 1.00 to 0.08 between weight at day 1 to weight at day 619, while for the Charollais, the correlations ranged from 1.00 to 0.05 from 1 to 640 days of age. Validation procedures were undertaken using a multitrait approach to examine the estimated breeding values when the correlation between the intercept and slope are fixed at different levels. The results indicated that fixing the correlation at 0.5 gave the most appropriate estimates for the Suffolk and Charollais datasets.

Novel approach for verification of a human PBPK modeling strategy using chimeric mice in the health risk assessment of epyrifenacil

In the human risk assessment by physiologically based pharmacokinetic modeling (PBPK), verification of the modeling strategy and confirmation of the reliability of the output data are important when the clinical data are not available. A new herbicide, epyrifenacil, is metabolized to S-3100-CA in mammals and causes hepatotoxicity in mice. S-3100-CA is transferred to the liver by transporters and eliminated by biliary excretion and metabolism. In the previous human PBPK research, we succeeded in predicting S-3100-CA pharmacokinetics by obtaining human hepatic parameters from chimeric mice with humanized liver after we checked the model's quantitative performance using mouse experimental data.To further enhance the reliability of human PBPK data, verification of the following two points was considered effective: 1) verification of model applicability to pharmacokinetics prediction in multiple animal species, and 2) verification of the parameter acquisition methods. In this study, we applied the same modeling strategy to rats, i.e., we obtained rat hepatic parameters for PBPK from chimeric mice with rat hepatocytes, not from rats. As the simulation results, rat internal dosimetry was precisely reproduced, although it tended to be slightly overestimated by approximately two times. From the results of the sensitivity analysis, this overestimation was mainly due to hepatic parameters from chimeric mice. Therefore, it is suggested that a similar slight prediction error may occur also in human PBPK using chimeric mice, but considering the degree of error, it can be said that our modeling strategy is robust and the predicted human internal dosimetry in the previous research is reliable.

Novel Approach to Automatic Identification and Detection of Aquatic Animal Species

Marine fisheries contribute greatly to the economic aspects of any country. India, having a coastline of almost 8000 KM, a surplus of fisheries potential could be estimated here. Because of this vast coastal area, active reporting of captured fishes is difficult through manual monitoring. Computer-aided approach is the best suitable option during the active season. This paper focuses on investigating an approach for identifying single as well as multiple aquatic animal species in a single image. Further a responsive web as well as mobile application are developed, in which the ML models are integrated. This will help users to access data as per their use. The method used YOLOv5n, a lightweight object detection algorithm, to detect these species. The trained model yielded mAP@0.5:0.95 intersection over union (IoU), and average precision (AP) for each species. The species’ AP varied as well. Few GFLOPs are used by YOLOv5n. This indicates that it is a scaled-down version capable of running on the 5.1 GFLOP Raspberry Pi 3B+. Despite employing substantially fewer GFLOPs, YOLOv5n outperformed Faster R-CNN.

Protein translation paradox: Implications in translational regulation of aging.

Protein translation is an essential cellular process playing key roles in growth and development. Protein translation declines over the course of age in multiple animal species, including nematodes, fruit flies, mice, rats, and even humans. In all these species, protein translation transiently peaks in early adulthood with a subsequent drop over the course of age. Conversely, lifelong reductions in protein translation have been found to extend lifespan and healthspan in multiple animal models. These findings raise the protein synthesis paradox: age-related declines in protein synthesis should be detrimental, but life-long reductions in protein translation paradoxically slow down aging and prolong lifespan. This article discusses the nature of this paradox and complies an extensive body of work demonstrating protein translation as a modulator of lifespan and healthspan.

Development of a multienzyme isothermal rapid amplification and lateral flow dipstick combination assay for bovine coronavirus detection.

Bovine coronavirus (BCoV) is a major cause of infectious disease in cattle, causing huge economic losses to the beef and dairy industries worldwide. BCoV can infect humans and multiple other species of animals. A rapid, reliable, and simple test is needed to detect BCoV infection in suspected farms. In this study, we developed a novel multienzyme isothermal rapid amplification (MIRA) and lateral flow dipstick (LFD) combination assay, targeting a highly conserved region of the viral nucleocapsid (N) gene for BCoV detection. The MIRA-LFD assay was highly specific and sensitive, comparable to a published reverse transcription quantitative PCR (RT-qPCR) assay for BCoV detection. Compared with the published RT-qPCR assay, the κ value of the MIRA-LFD assay in the detection of 192 cattle clinical samples was 0.982. The MIRA-LFD assay did not require sophisticated instruments and the results could be observed with eyes. Our results showed that the MIRA-LFD assay was a useful diagnostic tool for rapid on-site detection of BCoV.

One Health Investigation of SARS-CoV-2 in People and Animals on Multiple Mink Farms in Utah.

From July-November 2020, mink (Neogale vison) on 12 Utah farms experienced an increase in mortality rates due to confirmed SARS-CoV-2 infection. We conducted epidemiologic investigations on six farms to identify the source of virus introduction, track cross-species transmission, and assess viral evolution. Interviews were conducted and specimens were collected from persons living or working on participating farms and from multiple animal species. Swabs and sera were tested by SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and serological assays, respectively. Whole genome sequencing was attempted for specimens with cycle threshold values <30. Evidence of SARS-CoV-2 infection was detected by rRT-PCR or serology in ≥1 person, farmed mink, dog, and/or feral cat on each farm. Sequence analysis showed high similarity between mink and human sequences on corresponding farms. On farms sampled at multiple time points, mink tested rRT-PCR positive up to 16 weeks post-onset of increased mortality. Workers likely introduced SARS-CoV-2 to mink, and mink transmitted SARS-CoV-2 to other animal species; mink-to-human transmission was not identified. Our findings provide critical evidence to support interventions to prevent and manage SARS-CoV-2 in people and animals on mink farms and emphasizes the importance of a One Health approach to address emerging zoonoses.

In Silico Analysis of Tetrodotoxin Binding in Voltage-Gated Sodium Ion Channels from Toxin-Resistant Animal Lineages.

Multiple animal species have evolved resistance to the neurotoxin tetrodotoxin (TTX) through changes in voltage-gated sodium ion channels (VGSCs). Amino acid substitutions in TTX-resistant lineages appear to be positionally convergent with changes in homologous residues associated with reductions in TTX block. We used homology modeling coupled with docking simulations to test whether positionally convergent substitutions generate functional convergence at the level of TTX-channel interactions. We found little evidence that amino acids at convergent positions generated similar patterns among TTX-resistant animal lineages across several metrics, including number of polar contacts, polar contact position, and estimates of binding energy. Though binding energy values calculated for TTX docking were reduced for some TTX-resistant channels, not all TTX-resistant channels and not all of our analyses returned reduced binding energy values for TTX-resistant channels. Our results do not support a simple model of toxin resistance where a reduced number of bonds between TTX and the channel protein prevents blocking. Rather models that incorporate flexibility and movement of the protein overall may better describe how homologous substitutions in the channel cause changes in TTX block.

Animals, Angelenos, and the Arbitrary

AbstractMultispecies entanglement has been a major research focus in environmental humanities, aiming to rethink ontological and ethical possibilities, especially in urban settings, by attending to speculative other-than-human futures. This article dwells on already existing entanglements of multiple species of animals in Los Angeles, using empirical data (conversations from the social media platform Nextdoor) to describe these entanglements according to a fourfold framework—spatial, emotional, behavioral, and political. Drawing on the political philosophy of nondomination, it argues that existing entanglements are primarily arbitrary in a political sense, and that moving beyond them will require reducing this arbitrariness, even it if it means restricting human freedom or introducing new forms of control over animals, for a more-than-human city to be just.

Comparative analysis of single cell lung atlas of bat, cat, tiger, and pangolin.

Horseshoe bats (Rhinolophus sinicus) might help maintain coronaviruses severely affecting human health, such as severe acute respiratory syndrome coronavirus (SARS-CoV). Bats may be more tolerant of viral infection than other mammals due to their unique immune system, but the exact mechanism remains to be fully explored. During the coronavirus disease 2019 (COVID-19) pandemic, multiple animal species were diseased by coronavirus infection, especially in the respiratory system. Herein, a comparative analysis with single nucleus transcriptomic data of the lungs across four species, including horseshoe bat, cat, tiger, and pangolin, were conducted. The distribution of entry factors for twenty-eight respiratory viruses was characterized for the four species. Our findings might increase our understanding of the immune background of horseshoe bats.Graphical abstract Supplementary InformationThe online version contains supplementary material available at 10.1007/s10565-022-09771-9.

Lipidomics and transcriptomics insight into impacts of microplastics exposure on hepatic lipid metabolism in mice

Microplastics (MPs), the emerging environmental pollutants, have attracted global attention due to the potential public health challenge and ecological security risk. Recent studies suggested liver as a vulnerable organ to MPs exposure, evidenced by abnormal hepatic lipid metabolism upon MPs intake in multiple animal species. However, the specific changes of lipid metabolism in mammalian livers, as well as the underlying mechanisms, remain to be elucidated. In the present study, C57BL/6 mice were randomly assigned to normal drinking water or drinking water containing 100 μg L−1 or 1000 μg L−1 polystyrene (PS) MPs for 8 weeks. MPs exposure exerted no significant effect on body weight, serum triglyceride or total cholesteryl esters. However, mice showed impaired glucose tolerance and hepatic lipid deposition in response to high-dose MPs administration. Further lipidomic analysis showed significant alteration in hepatic lipid species particularly with free fatty acids (FFAs) and triacylglycerols (TAGs) in mice exposed to MPs. Meanwhile, the liver transcriptional profile indicated MPs exposure-induced differentially expressed genes (DEGs) were enriched in pathways of lipid metabolism and unfolded protein response. Furthermore, most altered lipid species were significantly correlated with DEGs enriched in lipid metabolic signaling. These findings provide lipidomic and transcriptional signatures of liver in response to MPs exposure, which will shed light on further understanding of the metabolic toxicity of MPs.

Immunosorbent assay for detection of Trypanosoma evansi infection in multiple host species using chimeric protein A/G conjugate

Surra caused by an extracellular hemoflagellate, Trypanosoma evansi, leads to severe economic loss to livestock productivity in India. Among the various mammalian pathogenic trypanosomes, T. evansi has the widest host range.Usually, species specific conjugates are used in conventional indirect immunosorbent assay (ELISA) for diagnosis of T. evansi infection in different animal species. The aim of the study was to explore the use of non-species specific conjugates viz., protein A, G and chimeric protein A/G instead of species specific conjugates for development of indirect ELISAs. These assays were used for detection of antibodies against T. evansi infection in multiple animal species viz., equine, cattle, buffalo, dog, pig and camel. The functional affinities of serum immunoglobulins of six different animal species with different conjugates were determined by estimation of relative avidity index (RAI). The species specific conjugate based whole cell lysate- T. evansi antigen ELISA was considered as reference assay for comparison of sensitivity and specificity of non-species specific conjugates based ELISAs optimized in the present study. Data showed that serodiagnosis of T. evansi can be carried out by using chimeric protein A/G conjugate in multiple hosts viz., equine, buffalo, camel, pig and dog; protein G conjugate in equine and buffalo and protein A conjugate in camel, pig and dog. The relative diagnostic sensitivity and specificity for chimeric protein A/G conjugate varied from 60 to 100% and 79–100%, respectively for different livestock species. This approach might be helpful in monitoring and surveillance of T. evansi infection in multiple hosts in particular when host specific secondary antibody conjugates are not available. Investigations should be made in wild animals and other warm-blooded vertebrates to validate this hypothesis.

Molecular evolution and genetic characteristics of G3P[3] group A canine rotavirus isolated in Wuhan, China.

Rotaviruses can infect multiple animal species and have the potential for cross-recombination based on the segmented genome characteristics. To study the intra-host recombination and zoonotic potential of group A canine rotavirus (CRV), 438 samples were collected from domestic dogs in six animal hospitals and from stray dogs from October 2019 to May 2021 in Wuhan, China. Seven of the samples were positive (7/438) for group A CRV from which a CRV strain was successfully isolated in MA-104 cells. The genotype of the isolated strain was characterized by whole-genome sequencing showing that the genotype was group A CRV G3P[3]. According to the Rotavirus Classification Working Group (RCWG), the genomic constellation of the isolated CRV was G3-P[3]-I3-R3-C3-M3-A9-N2-T3-E3-H6, which belongs to the AU-1-like group with gene segments of AU-1-like and Cat 97-like strains. Based on the phylogenetic analysis of the 11 gene segments, we found that the different segments of the isolated group A CRV were closely related to several reassortment rotaviruses from different animal sources and bat strains. Based on the analysis of the molecular evolution and genetic characteristics, we concluded that the isolated strain might be a reassortment strain. These data further enrich our understanding of rotavirus molecular evolution and genetic characteristics in China.

Outlook of Covid-19 Curing through Structural and Electronic Properties of Natural Drugs

Humans and multiple species of animals must be infected by coronaviruses (positive-stranded RNA viruses) through enteric, respiratory, and central nervous system sickness with attractive targets for designing anti- Covid-19 conjunction. In this work, it has been investigated the compounds of luteolin-7- glucoside, curcumin, epicatechin-gallate, allicin, and zingerol as probable anti-pandemic Covid-19 receptors derived from medicinal plants. Anti-Covid-19 through the hydrogen bonding using the physicochemical features consisting of thermodynamic parameters, nuclear magnetic resonance analysis, and IR characteristics, of luteolin-7- glucoside, curcumin, epicatechin-gallate, allicin, and zingerol compounds binded to the fragment of Tyrosine-Methionine-Histidine as the selective area of the Covid-19, IR frequency and intensity of various normal modes of these structures have been estimated. The theoretical calculations were accomplished at different steps of theory to achieve the more accurate equilibrium geometrical consequences, and IR spectral analysis for each of the complex drugs of O-terminal or N-terminal auto-cleavage substrate were approved to clear the structural flexibility and substrate attaching of seven medicinal plants bonded to the active site of Covid-19 molecule. Comparing these compounds with two configurations prepares a new outlook for the design of substrate-based anti-targeting of Covid-19. This indicates a feasible model for designing a wide spectrum of anti-Covid-19 drugs. The compounds-based energy minimization of these materials has resulted in two more effectual lead compounds, N and O atoms, forming the hydrogen bonding (H-bonding) with potent anti- Covid-19. Finally, two medicinal ingredients of allicin, curcumin, luteolin-7- glucoside, and zingerol bonded to TMH have been directed to a Monte Carlo (MC) simulation and UV-Visible for estimating the absorbance of luteolin-7- glucoside, and epicatechin-gallate.

Evaluation of the theoretical risk of cross-reactivity among recently identified food allergens for dogs.

There is increasing evidence of cross-reactivity between allergens of close or distant species. The A-RISC (Allergens'-Relative Identity, Similarity and Cross-reactivity) index helps evaluate the risk of theoretical cross-reactivity between proteins of the same family among different species. To report the A-RISC indices for several food allergens of dogs between multiple food sources. We selected several recently characterised food allergens for dogs from fish and chicken (ACTA1, ALDOA, CKM, ENO3, GAPDH, PKM and TPI1), fish (TPM1/2), beef/lamb (PGM1) and corn/potato (WAXY). When quality sequence data were available, A-RISC indices were calculated between multiple animal and plant species that can be used as food sources. For the TPM subunits, A-RISC indices also were calculated with the environmental allergens Bla g 4 and Der f 10, and the Toxocara canis nematode. The A-RISC indices suggest a substantial theoretical risk of cross-reactivity between species for all allergens considered. For TPM, this risk also extends to the environmental and nematode allergens. There is a high theoretical risk of cross-reactivity between allergens of different species used as food sources. The clinical relevance of these elevated A-RISC indices should be studied further.

A nucleic acid detection assay combining reverse transcription recombinase-aided amplification with a lateral flow dipstick for the rapid visual detection of porcine deltacoronavirus

ABSTRACT Porcine deltacoronavirus (PDCoV) is an emerging enteropathogen causing severe diarrhoea, dehydration, and death in nursing piglets and enormous economic losses for the global swine industry. Furthermore, it can infect multiple animal species including humans. Therefore, a rapid, definitive diagnostic assay is required for the effective control of this zoonotic pathogen. To identify PDCoV, we developed a nucleic acid detection assay combining reverse transcription recombinase-aided amplification (RT-RAA) with a lateral flow dipstick (LFD) targeting the highly conserved genomic region in the ORF1b gene. The RT-RAA-LFD assay exhibited good PDCoV detection reproducibility and repeatability and could be completed within 11 min. Ten minutes at 40 °C was required for nucleic acid amplification and 1 min at room temperature was needed for the visual LFD readout. The assay specifically detected PDCoV and did not cross-react with any other major swine pathogens. The 95% limit of detection (LOD) was 3.97 median tissue culture infectious dose PDCoV RNA per reaction. This performance was comparable to that of a reference TaqMan-based real-time RT-PCR (trRT-PCR) assay for PDCoV. Of 149 swine small intestine, rectal swab, and serum samples, 71 and 75 tested positive for PDCoV according to RT-RAA-LFD and trRT-PCR, respectively. The diagnostic coincidence rate for both assays was 97.32% (145/149) and the kappa value was 0.946 (p < 0.001). Overall, the RT-RAA-LFD assay is a user-friendly diagnostic tool that can rapidly and visually detect PDCoV.

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

ABSTRACTThe 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.