Are pangolins scapegoats of the COVID‐19 outbreak‐CoV transmission and pathology evidence?

An RNA-Seq analysis of coronavirus in the skin of the Pangolin

Protection of the Critically Endangered East Asian Pangolin species is hampered by the vulnerability of captive individuals to infection. Studies have previously shown the pangolin to have a unique pseudogenisation of many immunity genes (including IFNE, IFIH1, cGAS, STING, TLR5, and TLR11), and we suspected that these losses could account for this vulnerability. Here we used RNA-Seq data to show the effect of these gene losses on the transcriptional response to a viral skin infection in a deceased pangolin. This virus is very closely related to the one causing the current COVID-19 pandemic in the human population (SARS-CoV2), and we found the most upregulated pathway was the same one previously identified in the lungs of SARS-CoV2-infected humans. As predicted, we found that the pathways downstream of the lost genes were not upregulated. For example, the pseudogenised interferon epsilon (IFNE) is known to be particularly important in epithelial immunity, and we show that interferon-related responses were not upregulated in the infected pangolin skin. We suggest that the pangolin's innate gene pseudogenisation is indeed likely to be responsible for the animal's vulnerability to infection.

Genome sequence analysis of Malayan pangolin (Manis javanica) forensic samples reveals the presence of Paraburkholderia fungorum sequences

Background

The Malayan pangolin (Manis javanica) is a placental mammal and is listed as Critically Endangered on the IUCN Red List of Threatened Species. Most previous attempts to breed pangolins in captivity have met with little success because of dietary issues, infections, and other complications, although a previous study reported breeding pangolins in captivity to the third generation. In our previous pangolin genome sequencing data analysis, we obtained a considerable amount of bacterial DNA from a pregnant female Malayan pangolin (named "UM3"), which was likely infected by Paraburkholderia fungorum-an agent of biodegradation and bioremediation in agriculture.

Methodology

Here, we further confirmed and characterized this bacterial species using PCR, histological staining, whole-genome sequencing, and bioinformatics approaches. PCR assays with in-house designed primer sets and 16S universal primers showed clear positive bands in the cerebrum, cerebellum, lung, and blood of UM3 suggesting that UM3 might have developed septicaemia. Histological staining showed the presence of Gram-negative rod-shaped bacteria in the pangolin brain and lungs, indicating the colonization of the bacteria in these two organs. In addition, PCR screening of UM3's fetal tissues revealed the presence of P. fungorum in the gastrocnemius muscle, but not in other tissues that we examined. We also sequenced and reconstructed the genome of pangolin P. fungorum, which has a genome size of 7.7 Mbps.

Conclusion

Our study is the first to present detailed evidence of the presence of P. fungorum in a pangolin and her fetus (although preliminary results were presented in our previous article). Here, we raise the concern that P. fungorum may potentially infect humans, especially YOPI (young, old, pregnant, and immunocompromised) people. Therefore, caution should be exercised when using this bacterial species as biodegradation or bioremediation agents in agriculture.

Antimicrobial resistance (AMR) as a form of human-wildlife conflict: Why and how nondomesticated species should be incorporated into AMR guidance

The challenge of antimicrobial resistance (AMR) continues to receive significant global attention as common infections become increasingly resistant to the drugs used to treat them. Once an infectious microbe has developed a mechanism of resistance, it can cause longer, more damaging infections which are more costly, time-consuming, and sometimes impossible to treat. Such impacts occur across the health of humans, animals, plants, and the environment. Thus, AMR is considered a One Health issue. However, current narratives on AMR focus on humans, food-producing animals, crops, and their immediate environments. Very little attention is given to wildlife in terms of the impact of AMR on their health, nor their role in the evolution and spread of AMR. This article (1) discusses an absence of wildlife in current AMR guidance, (2) suggests how this absence of wildlife could limit understanding of, and action on, AMR, (3) proposes that considering AMR as a form of human-wildlife conflict could enable AMR guidance to better incorporate wildlife into action planning and create a truly One Health approach to tackle AMR.

Susceptibility of Pets to SARS-CoV-2 Infection: Lessons from a Seroepidemiologic Survey of Cats and Dogs in Portugal

Betacoronavirus (β-CoV) are positive single-stranded RNA viruses known to infect mammals. In 2019, a novel zoonotic β-CoV emerged, the severe acute respiratory syndrome (SARS)-CoV-2. Although the most frequent SARS-CoV-2 transmission route is within humans, spillover from humans to domestic and wild animals has been reported, including cats (Felis catus), dogs (Canis lupus familiaris), and minks (Neovision vision). In order to understand the potential role of domestic animals in SARS-CoV-2 global transmission, as well their susceptibility to infection, a seroepidemiologic survey of cats and dogs in Portugal was conducted. Antibodies against SARS-CoV-2 were detected in 15/69 (21.74%) cats and 7/148 (4.73%) dogs. Of the SARS-CoV-2 seropositive animals, 11/22 (50.00%) were possibly infected by human-to-animal transmission, and 5/15 (33.33%) cats were probably infected by cat-to-cat transmission. Moreover, one dog tested positive for SARS-CoV-2 RNA. Data suggest that cats and dogs are susceptible to SARS-CoV-2 infection in natural conditions. Hence, a one-health approach is crucial in the SARS-CoV-2 pandemic to understand the risk factors beyond infection in a human-animal environment interface.

In the post-COVID-19 era, is the illegal wildlife trade the most serious form of trafficking?

Despite the immense impact of wildlife trafficking, comparisons of the profits, costs, and seriousness of crime consistently rank wildlife trafficking lower relative to human trafficking, drug trafficking and weapons trafficking. Using the published literature and current events, we make the case, when properly viewed within the context of COVID-19 and other zoonotic diseases transmitted from wildlife, that wildlife trafficking is the most costly and perhaps the most serious form of trafficking. Our synthesis should raise awareness of the seriousness of wildlife trafficking for humans, thereby inducing strategic policy decisions that boost criminal justice initiatives and resources to combat wildlife trafficking.

Positive selection as a key player for SARS-CoV-2 pathogenicity: Insights into ORF1ab, S and E genes

The human β-coronavirus SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China. It causes Covid-19 disease which has become pandemic. Each of the five-known human β-coronaviruses has four major structural proteins (E, M, N and S) and 16 non-structural proteins encoded by ORF1a and ORF1b together (ORF1ab) that are involved in virus pathogenicity and infectivity. Here, we performed detailed positive selection analyses for those six genes among the four previously known human β-coronaviruses and within 38 SARS-CoV-2 genomes to assess signatures of adaptive evolution using maximum likelihood approaches. Our results suggest that three genes (E, S and ORF1ab genes) are under strong signatures of positive selection among human β-coronavirus, influencing codons that are located in functional important protein domains. The E protein-coding gene showed signatures of positive selection in two sites, Asp 66 and Ser 68, located inside a putative transmembrane α-helical domain C-terminal part, which is preferentially composed by hydrophilic residues. Such Asp and Ser sites substitutions (hydrophilic residues) increase the stability of the transmembrane domain in SARS-CoV-2. Moreover, substitutions in the spike (S) protein S1 N-terminal domain have been found, all of them were located on the S protein surface, suggesting their importance in viral transmissibility and survival. Furthermore, evidence of strong positive selection was detected in three of the SARS-CoV-2 nonstructural proteins (NSP1, NSP3, NSP16), which are encoded by ORF1ab and play vital roles in suppressing host translation machinery, viral replication and transcription and inhibiting the host immune response. These results are insightful to assess the role of positive selection in the SARS-CoV-2 encoded proteins, which will allow to better understand the virulent pathogenicity of the virus and potentially identifying targets for drug or vaccine strategy design.

Exploitation Histories of Pangolins and Endemic Pheasants on Hainan Island, China: Baselines and Shifting Social Norms

Overexploitation is a critical threat to the survival of many species. The global demand for wildlife products has attracted considerable research attention, but regional species exploitation histories are more rarely investigated. We interviewed 169 villagers living around seven terrestrial nature reserves on Hainan Island, China, with the aim of reconstructing historical patterns of hunting and consumption of local wildlife, including the globally threatened Chinese pangolin (Manis pentadactyla) and Hainan peacock-pheasant (Polyplectron katsumatae), from the mid-20th century onwards. We aimed to better understand the relationship between these past activities and current consumption patterns. Our findings suggest that eating pangolin meat was not a traditional behaviour in Hainan, with past consumption prohibited by local myths about pangolins. In contrast, local consumption of peacock-pheasant meat was a traditional activity. However, later attitudes around hunting pangolins and peacock-pheasants in Hainan were influenced by pro-hunting policies and a state-run wildlife trade from the 1960s to the 1980s. These new social norms still shape the daily lifestyles and perceptions of local people towards wildlife consumption in Hainan today. Due to these specific historical patterns of wildlife consumption, local-adapted interventions such as promoting substitute meat choices and alternative livelihoods might be effective at tackling local habits of consuming wild meat. Our study highlights the importance of understanding the local historical contexts of wildlife use for designing appropriate conservation strategies.

Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review

SARS-CoV-2 is a new human coronavirus (CoV), which emerged in China in late 2019 and is responsible for the global COVID-19 pandemic that caused more than 97 million infections and 2 million deaths in 12 months. Understanding the origin of this virus is an important issue, and it is necessary to determine the mechanisms of viral dissemination in order to contain future epidemics. Based on phylogenetic inferences, sequence analysis and structure-function relationships of coronavirus proteins, informed by the knowledge currently available on the virus, we discuss the different scenarios on the origin-natural or synthetic-of the virus. The data currently available are not sufficient to firmly assert whether SARS-CoV2 results from a zoonotic emergence or from an accidental escape of a laboratory strain. This question needs to be solved because it has important consequences on the risk/benefit balance of our interactions with ecosystems, on intensive breeding of wild and domestic animals, on some laboratory practices and on scientific policy and biosafety regulations. Regardless of COVID-19 origin, studying the evolution of the molecular mechanisms involved in the emergence of pandemic viruses is essential to develop therapeutic and vaccine strategies and to prevent future zoonoses. This article is a translation and update of a French article published in Médecine/Sciences, August/September 2020 (10.1051/medsci/2020123).

Supplementary Information

The online version of this article (10.1007/s10311-020-01151-1) contains supplementary material, which is available to authorized users.

Comprehensive genome analysis of a pangolin-associated Paraburkholderia fungorum provides new insights into its secretion systems and virulence

Background

Paraburkholderia fungorum (P. fungorum) is a Gram-negative environmental species that has been commonly used as a beneficial microorganism in agriculture as an agent for biocontrol and bioremediation. Its use in agriculture is controversial as many people believe that it could harm human health; however, there is no clear evidence to support.

Methodology

The pangolin P. fungorum (pangolin Pf) genome has a genomic size of approximately 7.7 Mbps with N50 of 69,666 bps. Our study showed that pangolin Pf is a Paraburkholderia fungorum supported by evidence from the core genome SNP-based phylogenetic analysis and the ANI analysis. Functional analysis has shown that the presence of a considerably large number of genes related to stress response, virulence, disease, and defence. Interestingly, we identified different types of secretion systems in the genome of pangolin Pf, which are highly specialized and responsible for a bacterium’s response to its environment and in physiological processes such as survival, adhesion, and adaptation. The pangolin Pf also shared some common virulence genes with the known pathogenic member of the Burkholderiales. These genes play important roles in adhesion, motility, and invasion.

Conclusion

This study may provide better insights into the functions, secretion systems and virulence of this pangolin-associated bacterial strain. The addition of this genome sequence is also important for future comparative analysis and functional work of P. fungorum.