Isolation and characterization of a pangolin-borne HKU4-related coronavirus that potentially infects human-DPP4-transgenic mice.

We recently detected a HKU4-related coronavirus in subgenus Merbecovirus (named pangolin-CoV-HKU4-P251T) from a Malayan pangolin1. Here we report isolation and characterization of pangolin-CoV-HKU4-P251T, the genome sequence of which is closest to that of a coronavirus from the greater bamboo bat (Tylonycteris robustula) in Yunnan Province, China, with a 94.3% nucleotide identity. Pangolin-CoV-HKU4-P251T is able to infect human cell lines, and replicates more efficiently in cells that express human-dipeptidyl-peptidase-4 (hDPP4)-expressing and pangolin-DPP4-expressing cells than in bat-DPP4-expressing cells. After intranasal inoculation with pangolin-CoV-HKU4-P251, hDPP4-transgenic female mice are likely infected, showing persistent viral RNA copy numbers in the lungs. Progressive interstitial pneumonia developed in the infected mice, characterized by the accumulation of macrophages, and increase of antiviral cytokines, proinflammatory cytokines, and chemokines in lung tissues. These findings suggest that the pangolin-borne HKU4-related coronavirus has a potential for emerging as a human pathogen by using hDPP4.

Infantile hemangioma in a subadult Chinese pangolin: a case report.

BACKGROUND: Hemangiomas are a relatively common type of tumor in humans and animals. Various subtypes of hemangiomas have been described in the literature. The classification methods for hemangiomas differ between human and veterinary medicine, and the basis for tumor classification can be found in the literature. CASE PRESENTATION: This study describes a tumor in the subcutaneous tissue of the right dorsum of an artificially rescued juvenile Chinese pangolin. Computed tomography (CT) examination yielded the preliminary diagnosis of a vascular malformation, and surgery was performed to resect the tumor. Histopathological examination showed that the tumor mainly was consisted of adipose tissue, capillaries, and spindle cells in the fibrous stroma. Immunohistochemistry showed the positive expression of CD31, CD34, α-SMA, GLUT1 and WT-1 in the tumor tissue, and the tumor was eventually diagnosed as an infantile haemangioma. CONCLUSION: The final diagnosis of infantile hemangioma was depended on the histopathological immunohistochemical and CT examination of the neoplastic tissue. This is the first report of infantile hemangioma in a critically endangered species Chinese pangolin.

The anti-cancer effect and mechanism of animal scale-derived extract on malignant melanoma cells.

Melanoma is a type of cancer with abnormal proliferation of melanocytes and is one of the most diagnosed cancer types. In traditional Chinese medicine, pangolin scales have been used to treat various diseases, including human cancers. However, its efficacy has not been scientifically proven. Here we studied the anticancer effect and mechanism of pangolin scale extract (PSE) on melanoma cell lines using scientific approaches. Our cell viability assay shows that PSE exhibits up to approximately 50-80% inhibition on SK-MEL-103 and A375 melanoma cell lines. Mechanically, PSE inhibits melanoma cell proliferation, migration, and causes changes in cell morphology. The apoptosis assay showed a significant chromosomal condensation inside the PSE-treated melanoma cells. The sequencing and analysis of A375 melanoma cell transcriptomes revealed 3077 differentially expressed genes in the 6 h treatment group and 8027 differentially expressed genes in the 72 h treatment group. Transcriptome analysis suggests that PSE may cause cell cycle arrest in melanoma cells and promote apoptosis mainly by up-regulating the p53 signaling pathway and down-regulating the PI3K-Akt signaling pathway. In this study, the anticancer effect of PSE was demonstrated by molecular biological means. PSE shows a significant inhibition effect on melanoma cell proliferation and cell migration in vitro, causes cell cycle arrest and promotes apoptosis through p53 and PI3K-AKT pathways. This study provides better insights into the anti-cancer efficacy and underlying mechanism of PSE and a theoretical basis for mining anticancer compounds or the development of new treatments for melanoma in the future. It is worth noting that this study does not advocate the use of the pangolin scale for disease treatment, but only to confirm its usefulness from a scientific research perspective and to encourage subsequent research around the development of active compounds to replace pangolin scales to achieve the conservation of this endangered species.

Design of a bifunctional pan-sarbecovirus entry inhibitor targeting the cell receptor and viral fusion protein.

Development of highly effective antivirals that are robust to viral evolution is a practical strategy for combating the continuously evolved severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Inspired by viral multistep entry process, we here focus on developing a bispecific SARS-CoV-2 entry inhibitor, which acts on the cell receptor angiotensin converting enzyme 2 (ACE2) and viral S2 fusion protein. First, we identified a panel of diverse spike (S) receptor-binding domains (RBDs) and found that the RBD derived from Guangdong pangolin coronavirus (PCoV-GD) possessed the most potent antiviral potency. Next, we created a bispecific inhibitor termed RBD-IPB01 by genetically linking a peptide fusion inhibitor IPB01 to the C-terminal of PCoV-GD RBD, which exhibited greatly increased antiviral potency via cell membrane ACE2 anchoring. Promisingly, RBD-IPB01 had a uniformly bifunctional inhibition on divergent pseudo- and authentic SARS-CoV-2 variants, including multiple Omicron subvariants. RBD-IPB01 also showed consistently cross-inhibition of other sarbecoviruses, including SARS-CoV, PCoV-GD, and Guangxi pangolin coronavirus (PCoV-GX). RBD-IPB01 displayed low cytotoxicity, high trypsin resistance, and favorable metabolic stability. Combined, our studies have provided a tantalizing insight into the design of broad-spectrum and potent antiviral agent. IMPORTANCE Ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution and spillover potential of a wide variety of sarbecovirus lineages indicate the importance of developing highly effective antivirals with broad capability. By directing host angiotensin converting enzyme 2 receptor and viral S2 fusion protein, we have created a dual-targeted virus entry inhibitor with high antiviral potency and breadth. The inhibitor receptor-binding domain (RBD)-IPB01 with the Guangdong pangolin coronavirus (PCoV-GD) spike RBD and a fusion inhibitor IPB01 displays bifunctional cross-inhibitions on pseudo- and authentic SARS-CoV-2 variants including Omicron, as well as on the sarbecoviruses SARS-CoV, PCoV-GD, and Guangxi pangolin coronavirus. RBD-IPB01 also efficiently inhibits diverse SARS-CoV-2 infection of human Calu-3 cells and blocks viral S-mediated cell-cell fusion with a dual function. Thus, the creation of such a bifunctional inhibitor with pan-sarbecovirus neutralizing capability has not only provided a potential weapon to combat future SARS-CoV-2 variants or yet-to-emerge zoonotic sarbecovirus, but also verified a viable strategy for the designing of antivirals against infection of other enveloped viruses.

Comparative analyses and phylogenetic relationships of thirteen Pholidota species (Orchidaceae) inferred from complete chloroplast genomes.

BACKGROUND: The orchid genus Pholidota Lindl. ex Hook. is economically important as some species has long been used in traditional medicine. However, the systematic status of the genus and intergeneric relationships inferred from previous molecular studies are unclear due to insufficient sampling and lack of informative sites. So far, only limited genomic information has been available. The taxonomy of Pholidota remains unresolved and somewhat controversial. In this study, the complete chloroplast (cp.) genomes of thirteen Pholidota species were sequenced and analyzed to gain insight into the phylogeny of Pholidota and mutation patterns in their cp. genomes. RESULTS: All examined thirteen Pholidota cp. genomes exhibited typical quadripartite circular structures, with the size ranging from 158,786 to 159,781 bp. The annotation contained a total of 135 genes in each cp. genome, i.e., 89 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The codon usage analysis indicated the preference of A/U-ending codons. Repeat sequence analysis identified 444 tandem repeats, 322 palindromic repeats and 189 dispersed repeats. A total of 525 SSRs, 13,834 SNPs and 8,630 InDels were detected. Six mutational hotspots were identified as potential molecular markers. These molecular markers and highly variable regions are expected to facilitate future genetic and genomic studies. Our phylogenetic analyses confirmed the polyphyletic status of the genus Pholidota, with species grouped into four main clades: Pholidota s.s. was resolved as the sister to a clade containing species of Coelogyne; the other two clades clustered together with species of Bulleyia and Panisea, respectively; species P. ventricosa was placed at the basal position, deviated from all other species. CONCLUSION: This is the first study to comprehensively examine the genetic variations and systematically analyze the phylogeny and evolution of Pholidota based on plastid genomic data. These findings contribute to a better understanding of plastid genome evolution of Pholidota and provide new insights into the phylogeny of Pholidota and its closely related genera within the subtribe Coelogyninae. Our research has laid the foundation for future studies on the evolutionary mechanisms and classification of this economically and medicinally important genus.

A bat MERS-like coronavirus circulates in pangolins and utilizes human DPP4 and host proteases for cell entry.

It is unknown whether pangolins, the most trafficked mammals, play a role in the zoonotic transmission of bat coronaviruses. We report the circulation of a novel MERS-like coronavirus in Malayan pangolins, named Manis javanica HKU4-related coronavirus (MjHKU4r-CoV). Among 86 animals, four tested positive by pan-CoV PCR, and seven tested seropositive (11 and 12.8%). Four nearly identical (99.9%) genome sequences were obtained, and one virus was isolated (MjHKU4r-CoV-1). This virus utilizes human dipeptidyl peptidase-4 (hDPP4) as a receptor and host proteases for cell infection, which is enhanced by a furin cleavage site that is absent in all known bat HKU4r-CoVs. The MjHKU4r-CoV-1 spike shows higher binding affinity for hDPP4, and MjHKU4r-CoV-1 has a wider host range than bat HKU4-CoV. MjHKU4r-CoV-1 is infectious and pathogenic in human airways and intestinal organs and in hDPP4-transgenic mice. Our study highlights the importance of pangolins as reservoir hosts of coronaviruses poised for human disease emergence.

Discovery of novel papillomaviruses in the critically endangered Malayan and Chinese pangolins.

Pangolins are scaly and toothless mammals which are distributed across Africa and Asia. Currently, the Malayan, Chinese and Philippine pangolins are designated as critically endangered species. Although few pangolin viruses have been described, their viromes have received more attention following the discovery that they harbour sarbecoviruses related to SARS-CoV-2. Using large-scale genome mining, we discovered novel lineages of papillomaviruses infecting the Malayan and Chinese pangolins. We were able to assemble three complete circular papillomavirus genomes with an intact coding capacity and five additional L1 genes encoding the major capsid protein. Phylogenetic analysis revealed that seven out of eight L1 sequences formed a monophyletic group which is the sister lineage to the Tupaia belangeri papillomavirus 1, isolated from Yunnan province in China. Additionally, a single L1 sequence assembled from a Chinese pangolin was placed in a clade closer to Alphapapillomavirus and Omegapapillomavirus. Examination of the SRA data from 95 re-sequenced genomes revealed that 49.3% of Malayan pangolins and 50% of Chinese pangolins were positive for papillomavirus reads. Our results indicate that pangolins in South-East Asia are the hosts of diverse and highly prevalent papillomaviruses, and highlight the value of in silico mining of host sequencing data for the discovery of novel viruses.

Rapid screening and identification of viral pathogens in metagenomic data.

BACKGROUND: Virus screening and viral genome reconstruction are urgent and crucial for the rapid identification of viral pathogens, i.e., tracing the source and understanding the pathogenesis when a viral outbreak occurs. Next-generation sequencing (NGS) provides an efficient and unbiased way to identify viral pathogens in host-associated and environmental samples without prior knowledge. Despite the availability of software, data analysis still requires human operations. A mature pipeline is urgently needed when thousands of viral pathogen and viral genome reconstruction samples need to be rapidly identified. RESULTS: In this paper, we present a rapid and accurate workflow to screen metagenomics sequencing data for viral pathogens and other compositions, as well as enable a reference-based assembler to reconstruct viral genomes. Moreover, we tested our workflow on several metagenomics datasets, including a SARS-CoV-2 patient sample with NGS data, pangolins tissues with NGS data, Middle East Respiratory Syndrome (MERS)-infected cells with NGS data, etc. Our workflow demonstrated high accuracy and efficiency when identifying target viruses from large scale NGS metagenomics data. Our workflow was flexible when working with a broad range of NGS datasets from small (kb) to large (100 Gb). This took from a few minutes to a few hours to complete each task. At the same time, our workflow automatically generates reports that incorporate visualized feedback (e.g., metagenomics data quality statistics, host and viral sequence compositions, details about each of the identified viral pathogens and their coverages, and reassembled viral pathogen sequences based on their closest references). CONCLUSIONS: Overall, our system enabled the rapid screening and identification of viral pathogens from metagenomics data, providing an important piece to support viral pathogen research during a pandemic. The visualized report contains information from raw sequence quality to a reconstructed viral sequence, which allows non-professional people to screen their samples for viruses by themselves (Additional file 1).

Pyelonephritis and Cystic Endometrial Hyperplasia in a Captive Sunda Pangolin (Manis javanica).

The Sunda pangolin (Manis javanica) is one of the most trafficked animal species globally, and is listed as Critically Endangered by the IUCN. There is limited information on reproductive biology or pathology of this species. We now document the clinical and pathological features of pyelonephritis and cystic endometrial hyperplasia in one of these animals. Ultrasonographic examination revealed pathological changes in the kidneys and uterus. On histopathological examination, there was marked interstitial infiltration of macrophages, neutrophils and lymphocytes in kidney tissue, fibrinonecrotic ureteritis and mild endometrial hyperplasia. This first report of these urogenital lesions in this species will be valuable for the conduct of health and reproductive assessments of the Sunda pangolin, which inform conservation and ex-situ management of this species.

Chemical Constituents and their Antioxidant, Anti-Inflammatory and Anti-Acetylcholinesterase Activities from Pholidota cantonensis.

Alzheimer's disease (AD) has the third highest health expenditures after heart disease and cancer. It has emerged as a serious global health issue. The discovery of new drugs to prevent and treat AD is of utmost importance. Pholidota cantonensis is an edible medicinal plant consumed in China. It is widely used in traditional Chinese medicine to treat various diseases. P. cantonensis has been reported to have antioxidant, anti-inflammatory, antitumor and antibacterial activities. Among these properties, its potent antioxidant activity has attracted our attention, since oxidative stress is one of the important pathological mechanisms involved in AD. This study aimed to isolate the compounds from the active extract and evaluate their bioactivities. Fifteen compounds, including one new compound, were obtained. The isolates were tested for 2,2'-diphenyl-1-picrylhydrazyl (DPPH)/2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging activities, anti-acetylcholinesterase (anti-AChE) activities and inhibitory effects on nitrogen monoxide (NO) release in the BV-2 cells. Compounds 1, 2, 4, 6, 8, and 13-15 exhibited two kinds of AD-associated bioactivities. More importantly, compound 13 showed more potent NO inhibitory activity (IC50 = 0.72 ± 0.08 µM) than the positive control quercetin (IC50 = 12.94 ± 0.08 µM). Compound 13 also had a higher inhibitory rate (99.59 ± 0.43%) on AChE than that of the positive control galantamine (78.32 ± 1.16%) at the concentrate of 50 µg/mL. Our studies provide new insights into this plant in terms of its potential in the development of new multi-target anti-Alzheimer's disease (anti-AD) drugs.

Measuring fecal metabolites of endogenous steroids using ESI-MS/MS spectra in Taiwanese pangolin, (order Pholidota, family Manidae, Genus: Manis): A non-invasive method for endangered species.

Pangolins are 'keystone species' driven towards extinction due to a lack of profound awareness and illegal trade. The drivers urge for immediate development in the understanding of demographics and reproductive dynamics of this species. In this study, we developed and validated a quantitative method to measure pangolin fecal extracts using the electrospray (ESI-MS/MS) interface in positive ionization mode. The method aids in the measurement of hormones from the hypothalamic-pituitary-adrenal (HPA) and hypothalamic-pituitary-gonadal (HPG) axis, making it a possibly appropriate technique to understand the cross-talk between the axes. The study aims to measure the relative abundance of adrenal and gonadal hormones such as corticosterone, cortisol, estrone, estradiol-17ß, progesterone, testosterone, and a number of its metabolites. From the dried fecal extract, the principal metabolite identified from the estrogen family was estradiol-17ß, whereas the gestagen family revealed that the pregnane series is predominated in 5α-configuration. On the other hand, epiandrosterone was seen as the dominant form in the male fecal extracts. Additionally, the glucocorticoids are excreted majorly as corticosterone, but traces of cortisol are also present in both the male and female fecal samples. The physiological validation confirmed that the ESI-MS/MS technique is suitable to determine physiologically caused differences in the fecal steroid concentrations. Physiologically, the age structure in pangolin is not responsible for causing differences within gender. However, the results revealed that glucocorticoids might vary between the sexes, i.e., males have a higher relative abundance of glucocorticoids over females. Therefore, our studies show that some of the main adrenal and gonadal metabolites can be predicted by exploiting MS/MS, which can steer research to potentially assess the reproductive status of captive and free-ranging pangolin species.

Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis.

The Envelope (E) protein of SARS-CoV-2 is the most enigmatic protein among the four structural ones. Most of its current knowledge is based on the direct comparison to the SARS E protein, initially mistakenly undervalued and subsequently proved to be a key factor in the ER-Golgi localization and in tight junction disruption. We compared the genomic sequences of E protein of SARS-CoV-2, SARS-CoV and the closely related genomes of bats and pangolins obtained from the GISAID and GenBank databases. When compared to the known SARS E protein, we observed a significant difference in amino acid sequence in the C-terminal end of SARS-CoV-2 E protein. Subsequently, in silico modelling analyses of E proteins conformation and docking provide evidences of a strengthened binding of SARS-CoV-2 E protein with the tight junction-associated PALS1 protein. Based on our computational evidences and on data related to SARS-CoV, we believe that SARS-CoV-2 E protein interferes more stably with PALS1 leading to an enhanced epithelial barrier disruption, amplifying the inflammatory processes, and promoting tissue remodelling. These findings raise a warning on the underestimated role of the E protein in the pathogenic mechanism and open the route to detailed experimental investigations.

Cytosolic DNA sensing through cGAS and STING is inactivated by gene mutations in pangolins.

The release of DNA into the cytoplasm upon damage to the nucleus or during viral infection triggers an interferon-mediated defense response, inflammation and cell death. In human cells cytoplasmic DNA is sensed by cyclic GMP-AMP Synthase (cGAS) and Absent In Melanoma 2 (AIM2). Here, we report the identification of a "natural knockout" model of cGAS. Comparative genomics of phylogenetically diverse mammalian species showed that cGAS and its interaction partner Stimulator of Interferon Genes (STING) have been inactivated by mutations in the Malayan pangolin whereas other mammals retained intact copies of these genes. The coding sequences of CGAS and STING1 are also disrupted by premature stop codons and frame-shift mutations in Chinese and tree pangolins, suggesting that expression of these genes was lost in a common ancestor of all pangolins that lived more than 20 million years ago. AIM2 is retained in a functional form in pangolins whereas it is inactivated by mutations in carnivorans, the phylogenetic sister group of pangolins. The deficiency of cGAS and STING points to the existence of alternative mechanisms of controlling cytoplasmic DNA-associated cell damage and viral infections in pangolins.

COMPLICATIONS ASSOCIATED WITH PREGNANCY AND PARTURITION IN AFRICAN WHITE-BELLIED PANGOLINS (PHATAGINUS TRICUSPIS).

There are no studies to date on the normal reproductive physiology of African white-bellied pangolins (Phataginus tricuspis). As a reclusive species, little is known about normal gestation, successful parturition, and potential complications during pregnancy. Ten female P. tricuspis were diagnosed as pregnant and monitored under professional care. Five developed complications during pregnancies or during parturition and are detailed in this case series. Dystocia occurred in two dams each, with malposition of a singleton fetus. Both dams were successfully treated with surgical intervention by caesarian section. Of the two individuals, one fetus was nonviable, but the other neonate survived and was reared by the dam to weaning. A third pregnant female died during pregnancy from septicemia resulting in death of the preterm fetus. The two additional dams of the five gave birth to full-term neonates. One fetus was stillborn with evidence of fetal distress, and the other died immediately after birth (perinatal death) with undetermined etiology. Based on this case series, complications associated with pregnancy occur in P. tricuspis, indicating the need for further study and close monitoring during impending parturition.