The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening of animal cells could reveal the expression patterns of viral entry genes in different hosts. However, such exploration for SARS-CoV-2 remains limited. Here, we perform single-nucleus RNA sequencing for 11 non-model species, including pets (cat, dog, hamster, and lizard), livestock (goat and rabbit), poultry (duck and pigeon), and wildlife (pangolin, tiger, and deer), and investigated the co-expression of ACE2 and TMPRSS2. Furthermore, cross-species analysis of the lung cell atlas of the studied mammals, reptiles, and birds reveals core developmental programs, critical connectomes, and conserved regulatory circuits among these evolutionarily distant species. Overall, our work provides a compendium of gene expression profiles for non-model animals, which could be employed to identify potential SARS-CoV-2 target cells and putative zoonotic reservoirs.

Poaching and trafficking have a substantial negative impact on the population growth and range expansion of the Chinese pangolin (Manis pentadactyla). However, recently reported activities of Chinese pangolins in several sites of Guangdong province in China indicate a promising sign for the recovery of this threatened species. Here, we re-sequence genomes of 15 individuals and perform comprehensive population genomics analyses with previously published 22 individuals. These Chinese pangolins are found to be divided into three distinct populations. Multiple lines of evidence indicate the existence of a newly discovered population (CPA) comprises entirely of individuals from Guangdong province. The other two populations (CPB and CPC) have previously been documented. The genetic differentiation of the CPA and CPC is extremely large (F_ST = 0.541), which is larger than many subspecies-level differentiations. Even for the closer CPA and CPB, their differentiation (F_ST = 0.101) is still comparable with the population-level differentiation of many endangered species. Further analysis reveals that the CPA and CPB populations separate 2.5–4.0 thousand years ago (kya), and on the other hand, CPA and CPC diverge around 25–40 kya. The CPA population harbors more runs of homozygosity (ROHs) than the CPB and CPC populations, indicating that inbreeding is more prevalent in the CPA population. Although the CPC population has less mutational load than CPA and CPB populations, we predict that several Loss of Function (LoF) mutations will be translocated into the CPA or CPB populations by using the CPC as a donor population for genetic rescue. Our findings imply that the conservation of Chinese pangolins is challenging, and implementing genetic rescue among the three groups should be done with extreme caution.

The outbreak of 2019-nCoV pneumonia (COVID-19) in the city of Wuhan, China has resulted in more than 70,000 laboratory confirmed cases, and recent studies showed that 2019-nCoV (SARS-CoV-2) could be of bat origin but involve other potential intermediate hosts. In this study, we assembled the genomes of coronaviruses identified in sick pangolins. The molecular and phylogenetic analyses showed that pangolin Coronaviruses (pangolin-CoV) are genetically related to both the 2019-nCoV and bat Coronaviruses but do not support the 2019-nCoV arose directly from the pangolin-CoV. Our study also suggested that pangolin be natural host of Betacoronavirus , with a potential to infect humans. Large surveillance of coronaviruses in pangolins could improve our understanding of the spectrum of coronaviruses in pangolins. Conservation of wildlife and limits of the exposures of humans to wildlife will be important to minimize the spillover risks of coronaviruses from wild animals to humans.

Wildlife populations are spatially controlled and undergo frequent fluctuations in abundance and site occupation. A comprehensive understanding of dynamic species processes is essential for making appropriate wildlife management plans. Here, we used a multi-season model to describe the dynamics of occupancy estimates of the carnivores: North Chinese leopard (Panthera pardus japonensis, Gray, 1862), leopard cat (Prionailurus bengalensis, Kerr, 1792), and red fox (Vulpes vulpes, Linnaeus, 1758) in the Tieqiaoshan Nature Reserve, Shanxi Province, China, over a three-year study period using camera traps data. The occupancy probability of the North Chinese leopard did not markedly change with time as the occupancy equilibrium was constant or slightly enhanced. The occupancy of the leopard cat decreased with time. The occupancy equilibrium of the red fox alternately increased and decreased. However, all species presented a slight level of occupancy stability due to their small values of the rate of change in occupancy. Environmental factor and anthropogenic disturbances slightly influenced the occupancy of all species and the colonization and extirpation probability of the red fox. The colonization and extirpation for all species were relatively more strongly affected by the distances to villages and roads. Moreover, elevation increased the colonization and decreased the extirpation for the leopard cat. Species interaction factors increased with time for all species. The North Chinese leopard and the leopard cat avoided each other. The leopard cat and the red fox independently co-occurred. There was true coexistence between the North Chinese leopard and the red fox. This research confirmed that environmental factors and human perturbations are vital factors to consider in wild carnivores’ conservation and management.

Livestock depredation by large carnivores is a conventional human–wildlife conflict, both at the local and regional level. Many species of wildlife have become endangered because of this conflict. In this study, an investigation of livestock depredation was conducted for the north China leopard in and around Tieqiaoshan Provincial Nature Reserve in Shanxi Province between 2015 and 2018. Data were obtained from League Cat Forest Department records. Additionally, standardized, structured, and semi-structured questionnaires were used to collect data with the help of reserve field staff. The results show that there was a significant difference (p = 0.015) in livestock depredation in various seasons of the year; the highest depredation was recorded in spring, followed by summer. A significant difference (p = 0.02) was observed between cattle and other livestock species, showing that more cattle were killed by the north China leopard. Most of the livestock depredation occurred during late morning and evening, likely because the leopards are crepuscular. Residents in and around the reserve suffered a high economic loss, ranging between RMB 5000 and 10,000 (USD 706.76–1413.53) per year in terms of the estimated market price of the killed livestock. The attitudes of residents towards the north China leopard vary according to the economic activities of the locals, with about 76% of the livestock keepers reporting that the leopard is “very dangerous” and 8% of the arable farmers in and around the reserve indicating that leopard is “very dangerous.” We recommend that a system with local participants would ensure more effective management of human-north China leopard conflict, as it would allow local communities to take greater responsibility.

The Chinese pangolin (Manis pentadactyla) is a critically endangered scale-covered mammal belonging to the order Pholidota. Wild pangolins are notably susceptible to pathogen infection and are typically characterized by impoverished health. However, little is currently known regarding the viruses prevalent among pangolins. In this study, we report the detection of two subtypes of canine parvovirus type 2 (CPV-2), namely CPV-2a and CPV-2c, both of which caused severe diarrheal disease in two post-rescue pangolins with fatal consequences. As in CPV-2-infected dogs, intensive lesion of the mucosal layer of the small intestines is a prominent feature in infected pangolins. Moreover, the immunochemistry results demonstrated that CPV-2 antigens were distributed in the crypts of small intestine. Additionally, typical parvovirus-associated CPV-2 were detected after four passages in F81 cells, and typical parvovirus-like particles, approximately 20 nm in diameter, were observed in the cell supernatants. Phylogenetic analysis revealed that the VP2 viral protein sequences (GenBank accession number OP208805) isolated from one pangolin (termed P1) were classified as CPV-2c, with 99.8% identity to a CPV-2c strain (MN832850) isolated from a Taiwanese pangolin found in Taiwan Province. In contrast, VP2 sequences (#OP208806) obtained from the second pangolin (P2) were classified as CPV-2a, with 99.8% identity to a CPV-2a strain (KY386858) isolated from southern China. In this study, we thus confirmed the infection of pangolins with CPV-2c in mainland China and demonstrated that CPV-2a also can infect pangolins. Based on these findings, we recommend that further investigations should be conducted to establish the interspecies transmission of these viruses among wild pangolins, wild carnivores, and stray dogs.