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

Caserta, Leonardo Cardia; Martins, Mathias; Butt, Salman Latif; Hollingshead, Nicholas; Covaleda, Lina; Ahmed, Sohel; Everts, Mia R R; Schuler, Krysten L.; Diel, Diego G.

doi:10.1073/pnas.2215067120

Cited by 61 publications

(57 citation statements)

References 41 publications

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“…Since prior surveillance studies have reported RT-qPCR positivity rates of upwards of 30% in nasal swabs 4 and seropositivity rates of more than 40% 12,26 , it was initially surprising that no animals within the Vermont sample set were positive, especially during the 2022 season. However, recent work from Diel et al describing the spread of SARS-CoV-2 within deer in New York state during the 2021 and 2022 seasons showed only sporadic positives during 2021 and a significant increase (up to 20%) in the 2022 season 15 . Furthermore, the majority of positive cases were detected in the western half of New York and near New York City, the farthest regions geographically from the Vermont border 14 .…”

Section: Discussionmentioning

confidence: 95%

“…However, multiple recent studies in North America have shown that members of the Cervidae family are susceptible to SARS-CoV-2. We hypothesized that SARS-CoV-2 might be circulating in Vermont deer and wildlife, given the numerous reports of infections within wild deer populations 4,[9][10][11][12][13][14][15] , and laboratory infections showing vertical 16 and horizontal transmission 17 .…”

Section: Introductionmentioning

confidence: 99%

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Surveillance of Vermont wildlife in 2021-2022 reveals no detected SARS-CoV-2 viral RNA

Despres

Mills

Schmidt

et al. 2023

Preprint

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Previous studies have documented natural infections of SARS-CoV-2 in various domestic and wild animals. More recently, studies have been published noting the susceptibility of members of the Cervidae family, and infections in both wild and captive cervid populations. In this study, we investigated the presence of SARS-CoV-2 in mammalian wildlife within the state of Vermont. 739 nasal or throat samples were collected from wildlife throughout the state during the 2021 and 2022 harvest season. Data was collected from red and gray foxes (Vulpes vulples and Urocyon cineroargentus, respectively), fishers (Martes pennati), river otters (Lutra canadensis), coyotes (Canis lantrans), bobcats (Lynx rufus rufus), black bears (Ursus americanus), and white-tailed deer (Odocoileus virginianus). Samples were tested for the presence of SARS-CoV-2 via quantitative RT-qPCR using the CDC N1/N2 primer set and/or the WHO-E gene primer set. Our results indicate that no sampled wildlife were positive for SARS-CoV-2. This finding is surprising, given that most published North America studies have found SARS-CoV-2 within their deer populations. The absence of SARS-CoV-2 RNA in populations sampled here may provide insights in to the various environmental and anthropogenic factors that reduce spillover and spread in North American's wildlife populations.

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Section: Discussionmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

Surveillance of Vermont wildlife in 2021-2022 reveals no detected SARS-CoV-2 viral RNA

Despres

Mills

Schmidt

et al. 2023

Preprint

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“…Seven CoVs infect humans; two of the α-genus (the Duvinacovirus hCoVs 229E and the Setracovirus NL63) and five of the β-genus: the Sarbecoviruses severe acute respiratory syndrome (SARS)-CoVs 1 and 2, the latter responsible for a pandemic since 2019 [ 3 – 6 ]; the Merbecovirus Middle East respiratory syndrome (MERS) CoV; and the Embecoviruses hCoV-OC43 and -HKU1. Human CoVs have a zoonotic origin, with bats as key reservoir [ 7 ] and possibly other hosts [ 8 , 9 ]. Bat β-CoVs related to human CoVs belong to the Sarbecovirus , Nobecovirus , and Hibecovirus subgenera [ 10 – 12 ].…”

Section: Introductionmentioning

confidence: 99%

Intragenomic rearrangements involving 5′-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses

Patarca

Haseltine

2023

Virol J

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Background Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses that was first documented in an infectious isolate of the betacoronavirus SARS-CoV-2, obtained from 3 patients in Hong Kong that had a 5′-untranslated region segment at the end of the ORF6 gene that in its new location translated into an ORF6 protein with a predicted modified carboxyl terminus. While comparing the amino acid sequences of translated ORF8 genes in the GenBank database, we found a subsegment of the same 5′-UTR-derived amino acid sequence modifying the distal end of ORF8 of an isolate from the United States and decided to carry out a systematic search. Methods Using the nucleotide and in the case of SARS-CoV-2 also the translated amino acid sequence in three reading frames of the genomic termini of coronaviruses as query sequences, we searched for 5′-UTR sequences in regions other than the 5′-UTR in SARS-CoV-2 and reference strains of alpha-, beta-, gamma-, and delta-coronaviruses. Results We here report numerous genomic insertions of 5′-untranslated region sequences into coding regions of SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses, but not delta- or gammacoronaviruses. To our knowledge this is the first systematic description of such insertions. In many cases, these insertions would change viral protein sequences and further foster genomic flexibility and viral adaptability through insertion of transcription regulatory sequences in novel positions within the genome. Among human Embecorivus betacoronaviruses, for instance, from 65% to all of the surveyed sequences in publicly available databases contain inserted 5′-UTR sequences. Conclusion The intragenomic rearrangements involving 5′-untranslated region sequences described here, which in several cases affect highly conserved genes with a low propensity for recombination, may underlie the generation of variants homotypic with those of concern or interest and with potentially differing pathogenic profiles. Intragenomic rearrangements thus add to our appreciation of how variants of SARS-CoV-2 and other beta- and alphacoronaviruses may arise.

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“…Starting in 2020, SARS-CoV-2 was found in white-tailed deer [WTD; 1,2]. By 2021, there was evidence of regional transmission in WTD through a combination of ongoing deer-to-deer and human-to-deer transmission [2][3][4][5]. Endemic transmission of SARS-CoV-2 in WTD could position these populations as reservoir hosts, posing risk for variant persistence [4,6], evolution of new variants [7,8], and spillback into human populations [7][8][9].…”

Section: Introductionmentioning

confidence: 99%

“…Deer-to-deer transmission may occur within wild populations beyond the initial introduction period. Surveillance studies in WTD have shown persistence of SARS-CoV-2 alpha and gamma variants in populations 4-6 months after their peak circulation and extinction in the human population [4,5,17,18]. These data describing susceptibility and transmission capabilities of SARS-CoV-2 in WTD and the fact that WTD are abundant and share a variety of habitats with humans across the United States [19], highlight the need to understand potential infection dynamics of SARS-CoV-2 in WTD across the range of the species.…”

Section: Introductionmentioning

confidence: 99%

Epidemiological Dynamics of SARS-CoV-2 in White-tailed Deer

Hewitt

Wilson-Henjum

Collins

et al. 2023

Preprint

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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 infection of SARS-CoV-2 in North American white-tailed deer (Odocoileus virginianus; WTD) using a hierarchical epidemiological model in the eastern half of the United States. Our model found that male deer had higher positivity than female deer, and positivity was higher in counties with higher human population density or deer habitat. Estimated SARS-CoV-2 local epidemiological reproduction numbers were between 1 and 2.5 in most well-sampled counties, with local epidemics in WTD peaking earlier in the northeast and mid-Atlantic relative to the Midwest and Southeast. Similar peak infection prevalence times across many counties provided indirect evidence for widespread transmission via human-to-deer spillover, while the widespread high estimates of local epidemiological reproduction number suggested that sustained deer-to-deer transmission is also probable. The model estimated 10% of infected WTD were infected due to human infection pressure.

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

Cited by 61 publications

References 41 publications

Surveillance of Vermont wildlife in 2021-2022 reveals no detected SARS-CoV-2 viral RNA

Surveillance of Vermont wildlife in 2021-2022 reveals no detected SARS-CoV-2 viral RNA

Intragenomic rearrangements involving 5′-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses

Epidemiological Dynamics of SARS-CoV-2 in White-tailed Deer

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