Isolation and characterization of microsatellite markers in pangolins (Mammalia,Pholidota, Manis spp.)

Thirty‐four polymorphic dinucleotide microsatellite loci were developed in the Malayan pangolin Manis javanica. Of the 34 markers, 32 and 18 were also amplified, respectively, in the Chinese pangolin (Manis pentadactyla) and the African tree pangolin (Manis tricuspis). Analysis of 24 Malayan, 12 Chinese and 2 African tree pangolins showed high levels of variability (heterozygosity ranging from 0.321 to 0.708). These are the first available microsatellite markers in Pholidota and will be an invaluable tool for evolutionary and conservation genetic studies in pangolins.     

Monitoring the gestation period of rescued Formosan pangolin (Manis pentadactyla pentadactyla) with progesterone radioimmunoassay

Eight species of pangolin have been identified in the world. However, understanding of pangolin reproductive biology has been limited to fragmentary records. In this study, the concentration of serum progesterone in three pregnant and two nonpregnant rescued female Formosan pangolins (Manis pentadactyla pentadactyla) was monitored using a commercial progesterone radioimmunoassay kit. During gestation, the serum progesterone of pregnant pangolins A, B, and C remained at 28.5–55 ng/ml (n = 31 samples), 10.9–50.1 ng/ml (n = 34), and 12.4 and 33.5 ng/ml with a peak at 47.6 ng/ml (n = 19), respectively, whereas the serum progesterone of nonpregnant pangolins D and E remained at 1.99 ± 1.62 ng/ml (n = 80) and 2.27 ± 1.64 ng/ml (n = 27), respectively. From this study, it was found that female pangolin weighing as low as 2.14 kg was already capable of reproduction. For pregnant pangolins to give birth to viable offspring, their body weight must increase significantly, 63.89 and 134.0% in the study, from the time of inception or early pregnancy until parturition. In addition, study has found that both viable offspring were born fully developed and exceeded 80 g in weight. The period of gestation was found to be as short as 318 or longer than 372 days. Therefore, the Formosan pangolin should only be able to reproduce once a year. This study is the first insight into hormone assay for determining the gestation period of pangolin. Further investigations on the same subject are necessary to establish criteria for the recognition of reproductive status in pangolins. Zoo Biol 31:479–489, 2012. © 2011 Wiley Periodicals, Inc.     

2010-2020年中华穿山甲在中国的发现记录及保护现状

中国是中华穿山甲(Manis pentadactyla)历史分布区面积和野生种群数量最大的国家.中华穿山甲曾广泛见于我国长江以南各省,但20世纪中期以来,由于其甲片被作为贵重的中药材原料,加之地下野味市场的需求,大量非法捕猎使得我国野生穿山甲经历了剧烈的分布区缩减和种群下降.目前,中华穿山甲已被列为我国一级重点保护野生...     

中国兽类一新纪录--爪哇穿山甲

记述了来自中国云南的爪哇穿山甲Manis javanica,即中国兽类新纪录,标本收藏在中国科学院昆明动物研究所标本馆.     

New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and Metagenomics

Rattus norvegicus (R. norvegicus) are ubiquitous and their presence has several effects on the human populations in our urban areas on a global scale. Both historically and presently, this close interaction has facilitated the dissemination of many pathogens to humans, making screening for potentially zoonotic and emerging viruses in rats highly relevant. We have investigated faecal samples from R. norvegicus collected from urban areas using a protocol based on metagenomic enrichment of circular DNA genomes and subsequent sequencing. We found a new type of papillomavirus, with a L1 region 82% identical to that of the known R. norvegicus Papillomavirus 2. Additionally, we found 20 different circular replication associated protein (Rep)-encoding single stranded DNA (CRESS-DNA) virus-like genomes, one of which has homology to the replication-associated gene of Beak and feather disease virus. Papillomaviruses are a group of viruses known for their carcinogenic potential, and although they are known to infect several different vertebrates, they are mainly studied and characterised in humans. CRESS-DNA viruses are found in many different environments and tissue types. Both papillomaviruses and CRESS-DNA viruses are known to have pathogenic potential and screening for novel and known viruses in R. norvegicus could help identify viruses with pathogenic potential.     

A sequence-independent strategy for detection and cloning of circular DNA virus genomes by using multiply primed rolling-circle amplification

The discovery of novel viruses has often been accomplished by using hybridization-based methods that necessitate the availability of a previously characterized virus genome probe or knowledge of the viral nucleotide sequence to construct consensus or degenerate PCR primers. In their natural replication cycle, certain viruses employ a rolling-circle mechanism to propagate their circular genomes, and multiply primed rolling-circle amplification (RCA) with phi29 DNA polymerase has recently been applied in the amplification of circular plasmid vectors used in cloning. We employed an isothermal RCA protocol that uses random hexamer primers to amplify the complete genomes of papillomaviruses without the need for prior knowledge of their DNA sequences. We optimized this RCA technique with extracted human papillomavirus type 16 (HPV-16) DNA from W12 cells, using a real-time quantitative PCR assay to determine amplification efficiency, and obtained a 2.4 x 10(4)-fold increase in HPV-16 DNA concentration. We were able to clone the complete HPV-16 genome from this multiply primed RCA product. The optimized protocol was subsequently applied to a bovine fibropapillomatous wart tissue sample. Whereas no papillomavirus DNA could be detected by restriction enzyme digestion of the original sample, multiply primed RCA enabled us to obtain a sufficient amount of papillomavirus DNA for restriction enzyme analysis, cloning, and subsequent sequencing of a novel variant of bovine papillomavirus type 1. The multiply primed RCA method allows the discovery of previously unknown papillomaviruses, and possibly also other circular DNA viruses, without a priori sequence information.     

Conservation genomics reveals possible illegal trade routes and admixture across pangolin lineages in Southeast Asia

The use of genome-wide genetic markers is an emerging approach for informing evidence-based management decisions for highly threatened species. Pangolins are the most heavily trafficked mammals across illegal wildlife trade globally, but critically endangered Sunda pangolins (Manis javanica) have not been widely studied in insular Southeast Asia. We used?>?12,000 single nucleotide polymorphic markers (SNPs) to assign pangolin seizures from illegal trade of unknown origin to possible geographic sources via genetic clustering with pangolins of known origin. Our SNPs reveal three previously unrecognized genetic lineages of Sunda pangolins, possibly from Borneo, Java and Singapore/Sumatra. The seizure assignments suggest the majority of pangolins were traded from Borneo to Java. Using mitochondrial markers did not provide the same resolution of pangolin lineages, and to explore if admixture might explain these differences, we applied sophisticated tests of introgression using?>?2000 SNPs to investigate secondary gene flow between each of the three Sunda pangolin lineages. It is possible the admixture which we discovered is due to human-mediated movements of pangolins. Our findings impact a range of conservation actions, including tracing patterns of trade, repatriation of rescue animals, and conservation breeding. In order to conserve genetic diversity, we suggest that, pending further research, each pangolin lineage should as a precaution be protected and managed as an evolutionarily distinct conservation unit.     

中国穿山甲与爪哇穿山甲甲片异速生长分析及其在司法鉴定中的应用

甲片对于穿山甲具有重要的防护功能,其形态差异反映了穿山甲对不同环境的适应性进化。该文对35只中国穿山甲和119只爪哇穿山甲甲片干重的异速生长模式进行了比较分析。结果表明,爪哇穿山甲较中国穿山甲的甲片干重相对于头体长具有更高的异速生长速率(P=0.005):爪哇穿山甲的甲片干重相对于头体长具有正的异速生长速率(b=3.725,P=0.001),而中国穿山甲的甲片干重相对于头体长则是等速生长(b=3.105,P=0.054)。这可能是由于较低纬度地区生活的爪哇穿山甲较较高纬度地区生活的中国穿山甲受到了更大的捕食压力影响。由于穿山甲甲片是一种重要传统中药材原料,相关违法贸易案件频发,且数量巨大。为推算穿山甲的涉案个体数量,建议这两种穿山甲甲片干重与个体数的换算标准为中国穿山甲573.47g,爪哇穿山甲360.51g,但是当两种穿山甲大量甲片混合在一起时,建议采用上述两个参数的平均值,即466.99g,以此为穿山甲甲片贸易案件的司法鉴定以及司法审判中的定罪量刑提供依据。     

Construction, characterization and FISH mapping of a bacterial artificial chromosome library of Chinese pangolin (Manis pentadactyla)

Chinese pangolins as a representative species in the order Pholidota have highly specified morphological characters and occupy an important place in the mammalian phylogenetic tree. To obtain genomic data for this species, we have constructed a bacterial artificial chromosome (BAC) library of Chinese pangolin. The library contains 208,272 clones with an average insert size of 122.1 kb and represents approximately eight times the Chinese pangolin haploid genome (if we assume that the Chinese pangolins have a genome size similar to human). One hundred and twenty randomly-selected BAC clones were mapped onto Chinese pangolin chromosomes by fluorescence in situ hybridization (FISH), showing a largely unbiased chromosomal distribution. Several clones containing repetitive DNA and ribosomal DNA genes were also found. The BAC library and FISH mapped BAC clones are useful resources for comparative genomics and cytogenetics of mammals and in particular, the ongoing genome sequencing project of Chinese pangolins.     

Digesta retention time and recovery rates of ants and termites in Chinese pangolins (Manis pentadactyla)

Pangolins are myrmecophagous mammals whose biology and ecology remain poorly studied. Termite mandibles and ant head capsules are the two primary remains found in pangolin feces. Determining the retention time of insect cuticles is important for understanding the digestive physiology of pangolins, while determining the recovery rate of termites and ants in feces is required to estimate the number of these prey items that are consumed by pangolins. In this study, the authors conducted feeding trials with captive Chinese pangolins (Manis pentadactyla). Sixty grams of the fungus-growing termite Odontotermes formosanus (18,816 individuals) and 15–20 g of the yellow crazy ant Anoplolepis gracilipes (14,400–19,200 individuals) were fed to each pangolin. After feeding, pangolin feces were collected daily for 1 week. The authors also assessed the accuracy of using chromium (III) oxide powder (Cr₂O₃) as a proxy for determining gut passage time, as has been done in previous studies. The results showed that remaining termite mandibles and ant head capsules in feces peaked at 66 and 90 hr after feeding and their recovery rates were 0.35 ± 0.10 and 0.65 ± 0.04, respectively. In both feeding trials, the retention time of Cr₂O₃ was much shorter than that of the termite mandibles and ant head capsules, indicating that Cr₂O₃ is not an appropriate indicator for estimating food retention time of myrmecophagous animals. Our results revealed that the ant head capsules were preserved better in feces compared with the termite mandibles, suggesting that termites may be considerably underestimated in the feces of wild pangolins.     

Identification of a Novel Human Papillomavirus by Metagenomic Analysis of Samples from Patients with Febrile Respiratory Illness

As part of a virus discovery investigation using a metagenomic approach, a highly divergent novel Human papillomavirus type was identified in pooled convenience nasal/oropharyngeal swab samples collected from patients with febrile respiratory illness. Phylogenetic analysis of the whole genome and the L1 gene reveals that the new HPV identified in this study clusters with previously described gamma papillomaviruses, sharing only 61.1% (whole genome) and 63.1% (L1) sequence identity with its closest relative in the Papillomavirus episteme (PAVE) database. This new virus was named HPV_SD2 pending official classification. The complete genome of HPV-SD2 is 7,299 bp long (36.3% G/C) and contains 7 open reading frames (L2, L1, E6, E7, E1, E2 and E4) and a non-coding long control region (LCR) between L1 and E6. The metagenomic procedures, coupled with the bioinformatic methods described herein are well suited to detect small circular genomes such as those of human papillomaviruses.     

Identification of a novel bat papillomavirus by metagenomics

The discovery of novel viruses in animals expands our knowledge of viral diversity and potentially emerging zoonoses. High-throughput sequencing (HTS) technology gives millions or even billions of sequence reads per run, allowing a comprehensive survey of the genetic content within a sample without prior nucleic acid amplification. In this study, we screened 156 rectal swab samples from apparently healthy bats (n = 96), pigs (n = 9), cattles (n = 9), stray dogs (n = 11), stray cats (n = 11) and monkeys (n = 20) using a HTS metagenomics approach. The complete genome of a novel papillomavirus (PV), Miniopterus schreibersii papillomavirus type 1 (MscPV1), with L1 of 60% nucleotide identity to Canine papillomavirus (CPV6), was identified in a specimen from a Common Bent-wing Bat (M. schreibersii). It is about 7.5kb in length, with a G+C content of 45.8% and a genomic organization similar to that of other PVs. Despite the higher nucleotide identity between the genomes of MscPV1 and CPV6, maximum-likelihood phylogenetic analysis of the L1 gene sequence showed that MscPV1 and Erethizon dorsatum papillomavirus (EdPV1) are most closely related. Estimated divergence time of MscPV1 from the EdPV1/MscPV1 common ancestor was approximately 60.2–91.9 millions of years ago, inferred under strict clocks using the L1 and E1 genes. The estimates were limited by the lack of reliable calibration points from co-divergence because of possible host shifts. As the nucleotide sequence of this virus only showed limited similarity with that of related animal PVs, the conventional approach of PCR using consensus primers would be unlikely to have detected the novel virus in the sample. Unlike the first bat papillomavirus RaPV1, MscPV1 was found in an asymptomatic bat with no apparent mucosal or skin lesions whereas RaPV1 was detected in the basosquamous carcinoma of a fruit bat Rousettus aegyptiacus. We propose MscPV1 as the first member of the novel Dyolambda-papillomavirus genus.     

Molecular basis of cross‐species ACE2 interactions with SARS‐CoV‐2‐like viruses of pangolin origin

Pangolins have been suggested as potential reservoir of zoonotic viruses, including SARS‐CoV‐2 causing the global COVID‐19 outbreak. Here, we study the binding of two SARS‐CoV‐2‐like viruses isolated from pangolins, GX/P2V/2017 and GD/1/2019, to human angiotensin‐converting enzyme 2 (hACE2), the receptor of SARS‐CoV‐2. We find that the spike protein receptor‐binding domain (RBD) of pangolin CoVs binds to hACE2 as efficiently as the SARS‐CoV‐2 RBD in vitro. Furthermore, incorporation of pangolin CoV RBDs allows entry of pseudotyped VSV particles into hACE2‐expressing cells. A screen for binding of pangolin CoV RBDs to ACE2 orthologs from various species suggests a broader host range than that of SARS‐CoV‐2. Additionally, cryo‐EM structures of GX/P2V/2017 and GD/1/2019 RBDs in complex with hACE2 show their molecular binding in modes similar to SARS‐CoV‐2 RBD. Introducing the Q498H substitution found in pangolin CoVs into the SARS‐CoV‐2 RBD expands its binding capacity to ACE2 homologs of mouse, rat, and European hedgehog. These findings suggest that these two pangolin CoVs may infect humans, highlighting the necessity of further surveillance of pangolin CoVs.     

Factors influencing the habitat choice of pangolins (Manis spp.) in low land of Nepal

Pangolins in the genus Manis are nocturnal, burrowing, insectivorous mammals listed as Critically Endangered or Endangered by the International Union for Conservation of Nature. Two species of pangolins are found in Nepal: the Chinese pangolin (Manis pentadactyla) and Indian pangolin (Manis crassicaudata). Despite having high conservation priority, little attention has been given to conservation interventions of both species of pangolins found in the Terai region (low land) of Nepal. The present study assesses habitat use and factors affecting the habitat choice of pangolins in low land (Terai), Nepal, focusing on Amritdharapani Community Forest of Chitwan district. Pangolin burrows were used as the indirect signs, and opportunistic sampling method was used to record the burrows. After the identification of all occurrence sites (burrows) in the field, random points were generated excluding the points where burrows were recorded for sampling of nonoccurrence sites. A total of thirty‐nine burrows were observed at elevations ranging from 301 to 413 masl. Burrows were frequently associated with northwest aspects, gentle slope (15°–20°), moderate canopy cover (51%–75%), red‐colored soil, and acidic soils with pH 6.5–7. The burrows were most common in areas with weak human disturbance (i.e., 1,500–1,700 m from settlements), 800–1,200 m from roads, and within 300 m from a water source and within 20 m from the nearest termitarium. Distance to settlement, distance to road, soil pH, and canopy cover were found to affect the habitat choice of pangolins in the study area.     

Cis-Acting Negative RNA Elements on Papillomavirus Late mRNAs

Papillomaviruses comprise a large number of related small DNA tumor viruses with tropism for squamous epithelial cells. The papillomavirus replication cycle is strictly linked to the differentiation stages of the infected epithelial cells, and the expression of L1 and L2 capsid proteins from the viral late genes is primarily detected in the superficial layers of terminally differentiated cells. Expression of the L1 and L2 genes is blocked in nonterminally differentiated cells and the production of progeny virus is delayed until the infected cell reaches the upper strata of the squamous epithelium. This property presumably aids the papillomavirus to evade the immune surveillance of the host and allows establishment of persistent infections. Late gene expression levels are determined in part by regulatory RNA sequences on the papillomavirus mRNAs. This review focuses primarily on negativecis-acting elements on late papillomavirus mRNAs and their candidatetrans-acting factors. Identification and characterization of these components will contribute to our understanding of the regulated expression of papillomaviruses in mammalian cells.     

The Phylogeny of Living and Extinct Pangolins (Mammalia, Pholidota) and Associated Taxa: A Morphology Based Analysis

The present study was undertaken in order to effect a comprehensive phylogenetic analysis of the order Pholidota, examining seven of the eight currently recognized extant species (absent is Manis culionensis, formerly recognized as a subspecies of Manis javanica) and nearly all the well-known fossil taxa, and employing a wide range of osteological characters from the entire skeleton. In addition, the relationship of pangolins to several putative early Tertiary relatives, including palaeanodonts and the enigmatic “edentate” Eurotamandua joresi, were investigated. The goal of the study was to improve understanding of the systematics and the biogeographic and evolutionary history of the pangolins. A computer-based cladistic analysis of phylogenetic relationships among seven extant species of pangolins, five extinct pangolin species (including all but one of the well-preserved taxa), as well as Eurotamandua and two genera of metacheiromyid palaeanodonts, Palaeanodon and Metacheiromys, was performed based upon 395 osteological characteristics of the skull and postcranial skeleton. Characters were polarized via comparison to the following successive outgroups: the basal feliform carnivoran Nandinia binotata and the hedgehog Erinaceus sp., a eulipotyphlan laursiatherian placental. A revised classification is presented based on the results of the analysis. The results support the monophyly of Pholidota and Palaeanodonta by providing new anatomical characters that can serve to diagnose a pangolin/palaeanodont clade, termed here Pholidotamorpha. Pholidota is defined so as to include all living and fossil pangolins, including all three taxa of middle Eocene “edentates” from the Messel fauna of Germany, among them Eurotamandua joresi. The results do not support the monophyly of the remaining two Messel “edentates” originally placed in the same genus Eomanis, which is restricted to the type species Eomanis waldi. Euromanis, new genus, is named with Eomanis krebsi Storch and Martin, 1994, as the type species, to form a new combination Euromanis krebsi (Storch and Martin, 1994). The analysis strongly supports the monophyly of a crown clade of pangolins diagnosed by many anatomical synapomorphies, the family Manidae. This crown clade is sister to the family Patriomanidae, which includes two Tertiary taxa, Patriomanis americana and Cryptomanis gobiensis, within the superfamily Manoidea. The relationship of the Tertiary European pangolin Necromanis to these two families is unresolved. Within Manidae, the extant species are divided into three well-supported, monophyletic genera, Manis for the Asian pangolins, Smutsia for the African ground pangolins, and Phataginus for the African tree pangolins. The latter two form a monophyletic African assemblage, the subfamily Smutsiinae. The biogeographic implications of this phylogeny are examined. A European origin for Pholidota is strongly indicated. The fossil record of pangolins would seem to support a European origin for the modern forms, with subsequent dispersal into sub-Saharan African and then to southern Asia, and the phylogeny produced in this analysis is consistent with such a scenario.     

The emergence of a commercial trade in pangolins from Gabon

Recent seizures of illegally held wildlife indicate a mounting global trade in pangolins involving all eight species. Seizures of illegally traded African pangolins are increasing as wild populations of Asian species decline. We investigated trade in pangolins and law enforcement efforts in Gabon; a country likely to have intact wild populations of three of the four species of African pangolin. We compared village sales and trade chains between 2002‐2003 and 2014. Hunters reported pangolins to be the most frequently requested species in 2014, and the value of pangolins had increased at every point along their trade chain. In Libreville, giant pangolin prices increased 211% and arboreal pangolin prices 73% whilst inflation rose only 4.6% over the same period. We documented a low rate of interception of illegally traded pangolins despite increased law enforcement. Surveys of potential export routes detected exports across forest borders, in conjunction with ivory, but not through public transport routes. We conclude that whilst there is clear potential and likelihood that a wild pangolin export trade is emerging from Gabon, traditional bushmeat trade chains may not be the primary supply route. We recommend adjusting conservation policies and actions to impede further development of illegal trade within and from Gabon .     

Hematological parameters of four Chinese pangolins (Manis pentadactyla)

Hematological, differential, and blood chemistry values were determined in four Chinese pangolins (Manis pentadactyla), both at the time of their arrival and after more than 1 year in captivity. The data presented were derived from two samples obtained from each of four animals, and they provide a preliminary basis for comparison with clinical blood values from this and other pangolin species. No peculiar features were identified that distinguish this species from other mammals.     

Immunohistochemical Demonstration of Keratins in the Epidermal Layers of the Malayan Pangolin (Manis Javanica), with Remarks on the Evolution of the Integumental Scale Armour

Using immunohistochemistry, the study demonstrates the distribution of keratins (pankeratin with CK1-8, 10, 14-16, 19; keratins CK1, 5, 6, 9, 10; hair keratins AE13, AE14) in the epidermis of the Malayan pangolin (Manis javanica). A varying reaction spectrum was observed for pan-keratin, with body region-dependent negative to very strong reaction intensities. The dorsolateral epidermis exhibited positive reactions only in its vital layers, whereas the abdominal epidermis showed strong positive reactions in the soft two outer strata. The single acidic and basic-to-neutral (cyto)keratins produced clear variations compared to the pan-keratin tinging. For example, CK1 appeared in all epidermal layers of both body regions, except for the ventral stratum corneum, whereas CK5, 6, 9, 10 were restricted to the soft ventral epidermis. Here, distinctly positive reactions were confined to the stratum granulosum, except for CK6 that appeared in the soft stratum corneum. A different staining pattern was obvious for the hair keratins, i.e., positive reactions of AE13 concentrated only in the granular layer of the dorsal epidermis. In the abdominal epidermis, remarkable tinging for AE14 was visible in the stratum basale, decreasing toward the corneal layer, but was also found in the outer root sheath cells of the hair follicles in the ventral body part. Our findings are discussed related to the evolution of the horny dorsal scales of the pangolin, which may have started from the tail root, projecting forward to the head.Key words: keratinisation, epidermis, scale evolution, Malayan pangolin, immunohistochemistry     

Knowledge and Uses of African Pangolins as a Source of Traditional Medicine in Ghana

Traditional medicine has been practised in Ghana for centuries with the majority of Ghanaians still patronising the services of traditional healers. Throughout Africa a large number of people use pangolins as a source of traditional medicine, however, there is a dearth of information on the use of animals in folk medicine in Ghana, in particular the use of pangolins. The aim of this study was to determine the prevalent use of pangolins and the level of knowledge of pangolin use among traditional healers in Ghana for the treatment of human ailments. Data was gathered from 48 traditional healers using semi-structured interviews on the traditional medicinal use of pangolin body parts in the Kumasi metropolis of Ghana. The cultural importance index, relative frequency of citation, informant agreement ratio and use agreement values were calculated to ascertain the most culturally important pangolin body part as well as the level of knowledge dissemination among traditional healers with regards pangolin body parts. Our study revealed that 13 body parts of pangolins are used to treat various medicinal ailments. Pangolin scales and bones were the most prevalent prescribed body parts and indicated the highest cultural significance among traditional healing practices primarily for the treatment of spiritual protection, rheumatism, financial rituals and convulsions. Despite being classified under Schedule 1 of Ghana’s Wildlife Conservation Act of 1971 (LI 685), that prohibits anyone from hunting or being in possession of a pangolin, our results indicated that the use of pangolins for traditional medicinal purposes is widespread among traditional healers in Ghana. A study on the population status and ecology of the three species of African pangolins occurring in Ghana is urgently required in order to determine the impact this harvest for traditional medical purposes has on their respective populations as current levels appear to be unmonitored and unsustainable.