SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City
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Abstract
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.
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SciScore for 10.1101/2022.02.04.479189: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources The N and RBD genes, plus two streptavidin tags, were cloned into the mammalian expression vector pHL, and the recombinant proteins were produced in HEK (human embryo kidney) 293 cells as described previously9. HEKsuggested: None293suggested: NCI-DTP Cat# NCI-293TT, RRID:CVCL_1D85)Recombinant DNA Sentences Resources The N and RBD genes, plus two streptavidin tags, were cloned into the mammalian expression vector pHL, and the recombinant proteins were produced in HEK … SciScore for 10.1101/2022.02.04.479189: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources The N and RBD genes, plus two streptavidin tags, were cloned into the mammalian expression vector pHL, and the recombinant proteins were produced in HEK (human embryo kidney) 293 cells as described previously9. HEKsuggested: None293suggested: NCI-DTP Cat# NCI-293TT, RRID:CVCL_1D85)Recombinant DNA Sentences Resources The N and RBD genes, plus two streptavidin tags, were cloned into the mammalian expression vector pHL, and the recombinant proteins were produced in HEK (human embryo kidney) 293 cells as described previously9. pHLsuggested: RRID:Addgene_64171)Software and Algorithms Sentences Resources We used a semi-automated workflow that employed BioMek i7 liquid-handling workstations BioMeksuggested: (BioMek NXp NXp, RRID:SCR_019720)Briefly, the pipeline uses seqtk version 1.3-r116 for sequence trimming30, minimap version 2.131 for aligning reads against reference genome Wuhan-Hu-1 NC_045512.232,33, samtools version 1.1134 for sequence and file manipulation35, and iVar version 1.2.236 for primer trimming and variant calling37. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Data Analysis and Visualization: Serology data was analyzed using the z-test for differences in proportions and visualized using GraphPad Prism version 9.0 for macOS (GraphPad Software, San Diego, California USA). GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Study Limitations: The sample size in our study is small in adult deer with respect to effect size and observed variation, and the samples come predominantly from young male deer. Hence, the inferences that might be derived for the larger population are limited. The study is also a cross-sectional survey of opportunistically sampled white-tailed deer in highly urbanized settings during an epizootic, with potentially greater opportunities for contact with humans than deer in other environments. Hence, the findings may not be broadly representative outside of these settings. Finally, the current analyses and sampling strategy do not enable us to differentiate whether animals positive for both viral RNA and neutralizing antibodies are newly seroconverted or individuals re-infected. This will require detailed laboratory investigations or longitudinal studies. Study implications and future directions: Given the well-documented susceptibility of white-tailed deer to SARS-CoV-2 as observed with experimental and natural infections, including with different viral lineages and VoCs, the current finding of spillover of Omicron is not altogether surprising. Previous studies have suggested that white-tailed deer remain largely asymptomatic following experimental SARS-CoV-2 infection8,9. However, we note that these trials utilized ancestral SARS-CoV-2 lineages including the B.1 and Alpha VoCs, and outcomes of infection of white-tailed deer infected with more recent SARS-CoV-2 variants, suc...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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