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

Abstract

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.

Keywords: Odocoileus virginianus; SARS-CoV-2; animal reservoir; coronavirus; white-tail deer; zoonosis.

FIG 1

Map of Pennsylvania (PA), showing sampling sites and locations of SARS-CoV-2 positive deer. The counties comprising PA are outlined. The estimated proportion of positive samples is shown by the white-to-red color scale; counties that were not sampled are shown in gray. Total sample numbers and the number positive are written on each county sampled. The deer samples sequenced were assigned to variants as indicated by the rectangles outside the map; variant type is color-coded (teal for alpha/B1.1.7, purple/pink for delta/AY.#). The open boxes indicate sequences were available for the spike-only.

FIG 2

Base substitutions detected in sequences of deer from Pennsylvania. In (A) the proportions in humans sampled in the Delaware Valley is shown in blue along the top for alpha (upper) and delta (lower). Substitutions relative to the Wuhan strain references are shown by the colored boxes. The proportions in humans are shown by the blue shading in each box. Genes sampled are shown by the color code indicated along the bottom. Gray indicates lack of sampling. The bottom six rows of the delta samples indicate the spike-only amplicon sequences. (B) Types of base substitutions away from the Wuhan reference detected in humans (right) and deer (left). The proportions are shown by the color code at the left.

FIG 3

Analysis of alpha variant SARS-CoV-2 whole genome sequences from white-tailed deer, global nearest neighbor human-derived sequences, and Delaware Valley human-derived sequences. Phylogenetic analysis of alpha white-tailed deer-derived sequences, nearest global sequences, and contemporaneous human alpha lineage sequences from Delaware Valley, collected from 1/6/2021 to 11/16/2021(2 deer sequences, 200 global nearest neighbor human sequences, and 1239 contemporanious Delaware Valley human). Included in the contemporaneous Delaware Valley human samples are two examples of humans infected with the alpha variant during the delta wave as late as 10/17/2021 and 11/14/2021, although these samples are notably more similar to earlier human alpha sequences than the deer alpha sequences. Dear sequences are colored teal, contemporaneous Delaware Valley sequences are labeled gray, and global nearest neighbor sequences are uncolored.

FIG 4

Phylogeny of delta white-tailed deer sequences, nearest global human sequences, and human delta lineage sequences from Delaware Valley, collected from 10/14/2021 to 11/28/2021 (spanning the period of genomes obtained from deer). Included are 5 deer, 300 global nearest neighbor human, and 440 Delaware Valley human sequences. Deer sequences are marked in purple, Delaware Valley human sequences are marked in gray, and global nearest neighbor sequences are unmarked. Time resolved trees for each spillover are in Fig. S2.

FIG 5

Longitudinal comparison of deer variants and human variants. The bar plots show the progression of SARS-CoV-2 variants detected by genome sequencing in humans in eastern Delaware Valley from 1/31/2021 to 1/3/2022. The variants are color-coded according to the key to the right. The variants from white-tailed deer sequences are shown at the top of the figure, with the arrows showing the times of sampling. The deer isolates are color-coded on the deer icons as in the key; purple dots on deer icons indicate sequences identified as delta lineage by spike amplicon sequences but without whole genome sequences to further identify clade.