Molecular surveillance of potential SARS-CoV-2 reservoir hosts in wildlife rehabilitation centers

Abstract

Background: The COVID-19 pandemic, caused by SARS-CoV-2 infection, has become the most devastating zoonotic event in recent times, with negative impacts on both human and animal welfare as well as on the global economy. Although SARS-CoV-2 is considered a human virus, it likely emerged from animals, and it can infect both domestic and wild animals. This constitutes a risk for human and animal health including wildlife with evidence of SARS-CoV-2 horizontal transmission back and forth between humans and wild animals.

Aim: Molecular surveillance in different wildlife rehabilitation centers and wildlife associated institutions in Chile, which are critical points of animal-human interaction and wildlife conservation, especially since the aim of wildlife rehabilitation centers is to reintroduce animals to their original habitat.

Materials and methods: The survey was conducted in six WRCs and three wildlife associated institutions. A total of 185 samples were obtained from 83 individuals belonging to 15 different species, including vulnerable and endangered species. Each specimen was sampled with two different swabs: one oropharyngeal or nasopharyngeal according to the nostril diameter, and/or a second rectal sample. RNA was extracted from the samples and two different molecular assays were performed: first, a conventional RT-PCR with pan-coronavirus primers and a second SARS-CoV-2 qPCR targeting the N and S genes.

Results: All 185 samples were negative for SARS-CoV-2.

Clinical relevance: This study constitutes the first report on the surveillance of SARS-CoV-2 from wildlife treated in rehabilitation centers in Chile, and supports the biosafety procedures adopted in those centers.

Keywords: COVID-19; Chile; SARS-CoV-2; wildlife conservation; wildlife rehabilitation centers.

Figure 1.

Geographical distribution of sampled animals. Each dot represents where the animal was found, and each diamond represents the location of Wildlife Rehabilitation Centers (WRC) where the animal was admitted for sampling (WRC1-WRC9). The color of each circle indicates the respective WRC where the animals were sampled.

Figure 2.

Susceptibility to SARS-CoV-2 infection of sampled animals based on published data (Islam et al. ; Palmer et al. ; Parolin et al. ; Villanueva-Saz et al. ; Fischhoff et al. 2021a; 2021b). Since there are no in silico or experimental susceptibility reports for most species (Galictis cuja, Pudu puda, Lontra felina, Lycalopex culpaeus, Lycalopex griseus, Lycalopex fulvipes, Otaria byronia, Arctocephalus australis, Arctocephalus philippi, Arctocephalus tropicalis, Leopardus guigna, and Leopardus colocola), susceptibility was estimated based on taxonomic family. Each color represents the proportion of sampled individuals in each susceptibility category.