1
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Randall RE, Young DF, Hughes DJ, Goodbourn S. Persistent paramyxovirus infections: in co-infections the parainfluenza virus type 5 persistent phenotype is dominant over the lytic phenotype. J Gen Virol 2023; 104:001916. [PMID: 37962188 PMCID: PMC10768688 DOI: 10.1099/jgv.0.001916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Parainfluenza virus type 5 (PIV5) can either have a persistent or a lytic phenotype in cultured cells. We have previously shown that the phenotype is determined by the phosphorylation status of the phosphoprotein (P). Single amino acid substitutions at critical residues, including a serine-to-phenylalanine substitution at position 157 on P, result in a switch between persistent and lytic phenotypes. Here, using PIV5 vectors expressing either mCherry or GFP with persistent or lytic phenotypes, we show that in co-infections the persistent phenotype is dominant. Thus, in contrast to the cell death observed with cells infected solely with the lytic variant, in co-infected cells persistence is immediately established and both lytic and persistent genotypes persist. Furthermore, 10-20 % of virus released from dually infected cells contains both genotypes, indicating that PIV5 particles can package more than one genome. Co-infected cells continue to maintain both genotypes/phenotypes during cell passage, as do individual colonies of cells derived from a culture of persistently infected cells. A refinement of our model on how the dynamics of virus selection may occur in vivo is presented.
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Affiliation(s)
- Richard E. Randall
- School of Biology, Centre for Biomolecular Sciences, BMS Building, North Haugh, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Dan F. Young
- School of Biology, Centre for Biomolecular Sciences, BMS Building, North Haugh, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - David J. Hughes
- School of Biology, Centre for Biomolecular Sciences, BMS Building, North Haugh, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Steve Goodbourn
- Section for Pathogen Research, Institute for Infection and Immunity, St George’s, University of London, London SW17 0RE, UK
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2
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Nino Barreat JG, Kamada AJ, Reuben de Souza C, Katzourakis A. Discovery of novel papillomaviruses in the critically endangered Malayan and Chinese pangolins. Biol Lett 2023; 19:20220464. [PMID: 36596463 PMCID: PMC9810420 DOI: 10.1098/rsbl.2022.0464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
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.
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3
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Que T, Li J, He Y, Chen P, Lin W, He M, Yu L, Wu A, Tan L, Li Y, Hu Y, Tong Y. Human parainfluenza 3 and respiratory syncytial viruses detected in pangolins. Emerg Microbes Infect 2022; 11:1657-1663. [PMID: 35678141 PMCID: PMC9225696 DOI: 10.1080/22221751.2022.2086071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Pangolins have gained increasing global attention owing to their public health significance as potential zoonotic hosts since the identification of SARS-CoV-2-related viruses in them. Moreover, these animals could carry other respiratory viruses. In this study, we investigated the virome composition of 16 pangolins that died in 2018 with symptoms of pneumonia using metagenomic approaches. A total of eight whole virus sequences belonging to the Paramyxoviridae or Pneumoviridae families were identified, including one human parainfluenza virus 3, one human respiratory syncytial virus A, and six human respiratory syncytial virus B. All of these sequences showed more than 99% nucleotide identity with the virus isolated from humans at the whole-genome level and clustered with human viruses in the phylogenetic tree. Our findings provide evidence that pangolins are susceptible to HPIV3 and HRSV infection. Therefore, public awareness of the threat of pangolin-borne pathogens is essential to stop their human consumption and to prevent zoonotic viral transmission.
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Affiliation(s)
- Tengcheng Que
- Guangxi Zhuang Autonomous Region Terrestrial Wildlife Medical-aid and Monitoring Epidemic Diseases Research Center, Nanning, P.R. People's Republic of China
| | - Jing Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. People's Republic of China
| | - Yugan He
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. People's Republic of China
| | - Panyu Chen
- Guangxi Zhuang Autonomous Region Terrestrial Wildlife Medical-aid and Monitoring Epidemic Diseases Research Center, Nanning, P.R. People's Republic of China
| | - Wei Lin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. People's Republic of China
| | - Meihong He
- Guangxi Zhuang Autonomous Region Terrestrial Wildlife Medical-aid and Monitoring Epidemic Diseases Research Center, Nanning, P.R. People's Republic of China
| | - Lei Yu
- Guangxi Zhuang Autonomous Region Terrestrial Wildlife Medical-aid and Monitoring Epidemic Diseases Research Center, Nanning, P.R. People's Republic of China
| | - Aiqiong Wu
- Guangxi Zhuang Autonomous Region Terrestrial Wildlife Medical-aid and Monitoring Epidemic Diseases Research Center, Nanning, P.R. People's Republic of China
| | - Luohao Tan
- Guangxi Zhuang Autonomous Region Terrestrial Wildlife Medical-aid and Monitoring Epidemic Diseases Research Center, Nanning, P.R. People's Republic of China
| | - Yingjiao Li
- Guangxi Zhuang Autonomous Region Terrestrial Wildlife Medical-aid and Monitoring Epidemic Diseases Research Center, Nanning, P.R. People's Republic of China
| | - Yanling Hu
- School of Information and Management, Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, P. R. People's Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. People's Republic of China
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4
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Lina Z, Kai W, Fuyu A, Dongliang Z, Hailing Z, Xuelin X, Ce G, Hongmei Y, Yingjie K, Zhidong Z, Rongguang L, Yan H. Fatal canine parvovirus type 2a and 2c infections in wild Chinese pangolins (Manis pentadactyla) in southern China. Transbound Emerg Dis 2022; 69:4002-4008. [PMID: 36070349 PMCID: PMC10087772 DOI: 10.1111/tbed.14703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 02/04/2023]
Abstract
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.
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Affiliation(s)
- Zhang Lina
- Eco-Engineering Department, Guangdong Eco-Engineering Polytechnic, Guangzhou, China
| | - Wang Kai
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - An Fuyu
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Zhang Dongliang
- Key Laboratory of Special Animal Epidemic Disease of Ministry of Agriculture and Rural Affairs, Institute of Special Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Zhang Hailing
- Key Laboratory of Special Animal Epidemic Disease of Ministry of Agriculture and Rural Affairs, Institute of Special Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xu Xuelin
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Guo Ce
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Yan Hongmei
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Kuang Yingjie
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Zhang Zhidong
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Lu Rongguang
- School of Medicine, Chinese University of Hongkong Shenzhen, Shenzhen, China
| | - Hua Yan
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
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5
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Shi YN, Li LM, Zhou JB, Hua Y, Zeng ZL, Yu YP, Liu P, Yuan ZG, Chen JP. Detection of a novel Pestivirus strain in Java ticks (Amblyomma javanense) and the hosts Malayan pangolin (Manis javanica) and Chinese pangolin (Manis pentadactyla). Front Microbiol 2022; 13:988730. [PMID: 36118205 PMCID: PMC9479695 DOI: 10.3389/fmicb.2022.988730] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Pangolins are endangered animals and are listed in the CITES Appendix I of the Convention International Trade Endangered Species of Wild Fauna and Flora as well as being the national first-level protected wild animal in China. Based on a few reports on pangolins infected with pestiviruses of the Flaviviridae family, Pestivirus infections in pangolins have attracted increasing attention. Pangolin pestivirus is a pathogen that may cause diseases such as acute diarrhea and acute hemorrhagic syndrome. To better understand the epidemiology and genomic characterization of pestiviruses carried by pangolins, we detected pestiviruses in dead Malayan pangolin using metavirome sequencing technology and obtained a Pestivirus sequence of 12,333 nucleotides (named Guangdong pangolin Pestivirus, GDPV). Phylogenetic tree analysis based on the entire coding sequence, NS3 gene or RdRp gene sequences, showed that GDPV was closely related to previously reported pangolin-derived Pestivirus and clustered into a separate branch. Molecular epidemiological investigation revealed that 15 Pestivirus-positive tissues from two pangolins individuals with a positivity rate of 5.56%, and six Amblyomma javanense carried pestiviruses with a positivity rate of 19.35%. Moreover, the RdRp gene of the Pestivirus carried by A. javanense showed a high similarity to that carried by pangolins (93–100%), indicating A. javanense is likely to represent the vector of Pestivirus transmission. This study expands the diversity of viruses carried by pangolins and provides an important reference value for interrupting the transmission route of the virus and protecting the health of pangolins.
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Affiliation(s)
- Yuan-Ni Shi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Lin-Miao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Jia-Bin Zhou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Yan Hua
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, Guangdong, China
| | - Zhi-Liao Zeng
- Shenzhen Management Bureau of Natural Reserve, Shenzhen, Guangdong, China
| | - Ye-Pin Yu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Ping Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Zi-Guo Yuan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- *Correspondence: Zi-Guo Yuan,
| | - Jin-Ping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Jin-Ping Chen,
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6
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Shi W, Shi M, Que TC, Cui XM, Ye RZ, Xia LY, Hou X, Zheng JJ, Jia N, Xie X, Wu WC, He MH, Wang HF, Wei YJ, Wu AQ, Zhang SF, Pan YS, Chen PY, Wang Q, Li SS, Zhong YL, Li YJ, Tan LH, Zhao L, Jiang JF, Hu YL, Cao WC. Trafficked Malayan pangolins contain viral pathogens of humans. Nat Microbiol 2022; 7:1259-1269. [PMID: 35918420 PMCID: PMC9352580 DOI: 10.1038/s41564-022-01181-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 06/21/2022] [Indexed: 12/03/2022]
Abstract
Pangolins are the most trafficked wild animal in the world according to the World Wildlife Fund. The discovery of SARS-CoV-2-related coronaviruses in Malayan pangolins has piqued interest in the viromes of these wild, scaly-skinned mammals. We sequenced the viromes of 161 pangolins that were smuggled into China and assembled 28 vertebrate-associated viruses, 21 of which have not been previously reported in vertebrates. We named 16 members of Hunnivirus, Pestivirus and Copiparvovirus pangolin-associated viruses. We report that the l-protein has been lost from all hunniviruses identified in pangolins. Sequences of four human-associated viruses were detected in pangolin viromes, including respiratory syncytial virus, Orthopneumovirus, RotavirusA and Mammalian orthoreovirus. The genomic sequences of five mammal-associated and three tick-associated viruses were also present. Notably, a coronavirus related to HKU4-CoV, which was originally found in bats, was identified. The presence of these viruses in smuggled pangolins identifies these mammals as a potential source of emergent pathogenic viruses. Multiple pathogenic viruses are identified in a large set of pangolins, which shows that trading pangolins for scales or flesh may increase the risk of emergence of viral infections.
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Affiliation(s)
- Wenqiang Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Mang Shi
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, P. R. China
| | - Teng-Cheng Que
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, P. R. China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.,Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Run-Ze Ye
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P. R. China
| | - Luo-Yuan Xia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.,Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P. R. China
| | - Xin Hou
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, P. R. China
| | - Jia-Jing Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.,Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Xing Xie
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Wei-Chen Wu
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, P. R. China
| | - Mei-Hong He
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, P. R. China
| | - Hui-Feng Wang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Yong-Jie Wei
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, P. R. China
| | - Ai-Qiong Wu
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, P. R. China
| | - Sheng-Feng Zhang
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Yu-Sheng Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Pan-Yu Chen
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, P. R. China
| | - Qian Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.,Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P. R. China
| | - Shou-Sheng Li
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, P. R. China
| | - Yan-Li Zhong
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, P. R. China
| | - Ying-Jiao Li
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, P. R. China
| | - Luo-Hao Tan
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, Guangxi, P. R. China
| | - Lin Zhao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P. R. China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China. .,Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, P. R. China.
| | - Yan-Ling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, P. R. China. .,Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, P. R. China.
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China. .,Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, P. R. China. .,Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P. R. China.
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7
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He WT, Hou X, Zhao J, Sun J, He H, Si W, Wang J, Jiang Z, Yan Z, Xing G, Lu M, Suchard MA, Ji X, Gong W, He B, Li J, Lemey P, Guo D, Tu C, Holmes EC, Shi M, Su S. Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell 2022; 185:1117-1129.e8. [PMID: 35298912 PMCID: PMC9942426 DOI: 10.1016/j.cell.2022.02.014] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/10/2022] [Accepted: 02/10/2022] [Indexed: 12/27/2022]
Abstract
Game animals are wildlife species traded and consumed as food and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1,941 game animals, representing 18 species and five mammalian orders, sampled across China. From this, we identified 102 mammalian-infecting viruses, with 65 described for the first time. Twenty-one viruses were considered as potentially high risk to humans and domestic animals. Civets (Paguma larvata) carried the highest number of potentially high-risk viruses. We inferred the transmission of bat-associated coronavirus from bats to civets, as well as cross-species jumps of coronaviruses from bats to hedgehogs, from birds to porcupines, and from dogs to raccoon dogs. Of note, we identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence.
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Affiliation(s)
- Wan-Ting He
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.,These authors contributed equally
| | - Xin Hou
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.,These authors contributed equally
| | - Jin Zhao
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.,These authors contributed equally
| | - Jiumeng Sun
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Haijian He
- Agricultural College, Jinhua Polytechnic, Jinhua 320017, China
| | - Wei Si
- MOA Key Laboratory of Animal Virology, Zhejiang University, Hangzhou 310058, China
| | - Jing Wang
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Zhiwen Jiang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziqing Yan
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Gang Xing
- MOA Key Laboratory of Animal Virology, Zhejiang University, Hangzhou 310058, China
| | - Meng Lu
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Marc A. Suchard
- Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, the United States
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA 70118, USA
| | - Wenjie Gong
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China
| | - Biao He
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong 999077, China
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | - Deyin Guo
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Changchun Tu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Senior authors,Correspondence: Shuo Su (); Mang Shi (); and Edward C. Holmes ()
| | - Mang Shi
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.
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8
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Ning S, Dai Z, Zhao C, Feng Z, Jin K, Yang S, Shen Q, Wang X, Sun R, Zhang W. Novel putative pathogenic viruses identified in pangolins by mining metagenomic data. J Med Virol 2022; 94:2500-2509. [PMID: 34978087 DOI: 10.1002/jmv.27564] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/17/2021] [Accepted: 12/28/2021] [Indexed: 12/30/2022]
Abstract
The pangolin is the only scaly mammal in the world and also an important reservoir of pathogenic viruses. Habitat loss and poaching have been shrinking the survival range of pangolins. More information on pangolin virus populations is needed to better understand and assess potential disease risks. In this study, viral metagenomic data were used to reinvestigate the virome in pangolin lung tissue. Complete genome sequences of two novel anelloviruses were acquired and clustered with the referenced feline strains belonging to genus Tettorquevirus and genus Etatorquevirus, respectively. Two genomes belonging to the genus Gemykibivirus, and species Bat-associated cyclovirus 9 were detected, respectively. One genome with a large contig belonging to the genus Senecavirus were also characterized, according to phylogenetic analysis, which can be presumed to be a novel species. In addition, a full genome of endogenous retroviruse (ERV) was assembled from the lungs of pangolin, and this virus may have the possibility of cross-species transmission during the evolution. This virological investigation has increased our understanding of the virome carried by pangolins and provided a reference baseline for possible zoonotic infectious diseases in the future.
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Affiliation(s)
- Songyi Ning
- Donghai County People's Hospital, Jiangsu University, Donghai, Jiangsu, China
| | - Ziyuan Dai
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Chunyan Zhao
- Nursing School, Wuxi Taihu University, Wuxi, Jiangsu, China
| | - Zhanghao Feng
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Kexin Jin
- School of Mathematical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Runfeng Sun
- Donghai County People's Hospital, Jiangsu University, Donghai, Jiangsu, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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9
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Liu F, Wang Q, Shan H. Rescue of dual reporter-tagged parainfluenza virus 5 as tool for rapid screening of antivirals in vitro. Vet Microbiol 2021; 259:109154. [PMID: 34237497 DOI: 10.1016/j.vetmic.2021.109154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/13/2021] [Indexed: 11/16/2022]
Abstract
Parainfluenza virus 5 (PIV5) belongs to the genus Orthorubulavirus in the family Paramyxoviridae. PIV5 can infect a range of mammals, but induce mild or even unobservable clinical signs in some animals, except kennel cough in dogs. It is also able to infect a variety of cell lines, but causes minimal or even invisible cytopathic effects on many cells. Sometimes, owing to neither observable cytopathic effects in vitro nor typical clinical signs in vivo, the PIV5 is not easily usable for screening antiviral drugs. To solve this issue, we used reverse genetics to recover a dual reporter-tagged recombinant PIV5 that could simultaneously express enhanced green fluorescence protein (eGFP) and NanoLuc® luciferase (NLuc) in virus-infected cells. Both reporters were genetically stable during twenty serial passages of virus in MDBK cells. The eGFP allowed us to observe virus-infected MDBK cells in real time, and moreover the NLuc made it possible to quantify the degree of viral replication for determining antiviral activity of a given drug. Subsequently, the recombinant PIV5 was used for antiviral assays on five common drugs, i.e., ribavirin, apigenin, 1-adamantylamine hydrochloride, moroxydine hydrochloride and tea polyphenol. The results showed that only the ribavirin had an anti-PIV5 effect in MDBK cells. This study proposed a novel method for rapid screening (or prescreening) of anti-PIV5 drugs.
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Affiliation(s)
- Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
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10
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Chang YC, Lin ZY, Lin YX, Lin KH, Chan FT, Hsiao ST, Liao JW, Chiou HY. Canine Parvovirus Infections in Taiwanese Pangolins ( Manis pentadactyla pentadactyla). Vet Pathol 2021; 58:743-750. [PMID: 33866880 DOI: 10.1177/03009858211002198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Canine parvovirus type 2 (CPV-2) is among the most important and highly contagious pathogens that cause enteric or systemic infections in domestic and nondomestic carnivores. However, the spillover of CPV-2 to noncarnivores is rarely mentioned. Taiwanese pangolins (Manis pentadactyla pentadactyla) are threatened due to habitat fragmentation and prevalent animal trafficking. Interactions between Taiwanese pangolins, humans, and domestic animals have become more frequent in recent years. However, information about the susceptibility of pangolins to common infectious agents of domestic animals has been lacking. From October 2017 to June 2019, 4 pangolins that were rescued and treated in wildlife rescue centers in central and northern Taiwan presented with gastrointestinal signs. Gross and histopathological examination revealed the main pathologic changes to be necrotic enteritis with involvement of the crypts in all intestinal segments in 2 pangolins. By immunohistochemistry for CPV-2, there was positive labeling of cryptal epithelium throughout the intestine, and immunolabeling was also present in epidermal cells adjacent to a surgical amputation site, and in mononuclear cells in lymphoid tissue. The other 2 pangolins had mild enteritis without crypt involvement, and no immunolabeling was detected. The nucleic acid sequences of polymerase chain reaction (PCR) amplicons from these 4 pangolins were identical to a Chinese CPV-2c strain from domestic dogs. Quantitative PCR revealed a higher ratio of CPV-2 nucleic acid to internal control gene in the 2 pangolins with severe intestinal lesions and positive immunoreactivity. Herein, we present evidence of CPV-2 infections in pangolins.
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Affiliation(s)
| | - Zhi Yi Lin
- 34916National Chung Hsing University, Taichung
| | - Yan Xiu Lin
- 34916National Chung Hsing University, Taichung
| | - Kuei Hsien Lin
- Endemic Species Research Institute, 56086Council of Agriculture, Chichi
| | - Fang Tse Chan
- Endemic Species Research Institute, 56086Council of Agriculture, Chichi
| | - Shun Ting Hsiao
- Endemic Species Research Institute, 56086Council of Agriculture, Chichi
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11
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Lee J, Hughes T, Lee MH, Field H, Rovie-Ryan JJ, Sitam FT, Sipangkui S, Nathan SKSS, Ramirez D, Kumar SV, Lasimbang H, Epstein JH, Daszak P. No Evidence of Coronaviruses or Other Potentially Zoonotic Viruses in Sunda pangolins (Manis javanica) Entering the Wildlife Trade via Malaysia. ECOHEALTH 2020; 17:406-418. [PMID: 33226526 PMCID: PMC7682123 DOI: 10.1007/s10393-020-01503-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 05/21/2023]
Abstract
The legal and illegal trade in wildlife for food, medicine and other products is a globally significant threat to biodiversity that is also responsible for the emergence of pathogens that threaten human and livestock health and our global economy. Trade in wildlife likely played a role in the origin of COVID-19, and viruses closely related to SARS-CoV-2 have been identified in bats and pangolins, both traded widely. To investigate the possible role of pangolins as a source of potential zoonoses, we collected throat and rectal swabs from 334 Sunda pangolins (Manis javanica) confiscated in Peninsular Malaysia and Sabah between August 2009 and March 2019. Total nucleic acid was extracted for viral molecular screening using conventional PCR protocols used to routinely identify known and novel viruses in extensive prior sampling (> 50,000 mammals). No sample yielded a positive PCR result for any of the targeted viral families-Coronaviridae, Filoviridae, Flaviviridae, Orthomyxoviridae and Paramyxoviridae. In the light of recent reports of coronaviruses including a SARS-CoV-2-related virus in Sunda pangolins in China, the lack of any coronavirus detection in our 'upstream' market chain samples suggests that these detections in 'downstream' animals more plausibly reflect exposure to infected humans, wildlife or other animals within the wildlife trade network. While confirmatory serologic studies are needed, it is likely that Sunda pangolins are incidental hosts of coronaviruses. Our findings further support the importance of ending the trade in wildlife globally.
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Affiliation(s)
- Jimmy Lee
- EcoHealth Alliance, 520 Eighth Avenue, Suite 1200, New York, NY, 10018, USA.
- Conservation Medicine, Unit 13H Villamas, Jalan Villamas, 47000, Sungai Buloh, Selangor, Malaysia.
| | - Tom Hughes
- EcoHealth Alliance, 520 Eighth Avenue, Suite 1200, New York, NY, 10018, USA
- Conservation Medicine, Unit 13H Villamas, Jalan Villamas, 47000, Sungai Buloh, Selangor, Malaysia
| | - Mei-Ho Lee
- EcoHealth Alliance, 520 Eighth Avenue, Suite 1200, New York, NY, 10018, USA
- Conservation Medicine, Unit 13H Villamas, Jalan Villamas, 47000, Sungai Buloh, Selangor, Malaysia
| | - Hume Field
- EcoHealth Alliance, 520 Eighth Avenue, Suite 1200, New York, NY, 10018, USA
| | - Jeffrine Japning Rovie-Ryan
- National Wildlife Forensic Laboratory, Department of Wildlife and National Parks (PERHILITAN), Peninsular Malaysia, KM 10, Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory, Department of Wildlife and National Parks (PERHILITAN), Peninsular Malaysia, KM 10, Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Symphorosa Sipangkui
- Sabah Wildlife Department, 5th Floor, B Block, Wisma MUIS, 88100, Kota Kinabalu, Sabah, Malaysia
| | - Senthilvel K S S Nathan
- Sabah Wildlife Department, 5th Floor, B Block, Wisma MUIS, 88100, Kota Kinabalu, Sabah, Malaysia
| | - Diana Ramirez
- Sabah Wildlife Department, 5th Floor, B Block, Wisma MUIS, 88100, Kota Kinabalu, Sabah, Malaysia
| | - Subbiah Vijay Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Helen Lasimbang
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Jonathan H Epstein
- EcoHealth Alliance, 520 Eighth Avenue, Suite 1200, New York, NY, 10018, USA
| | - Peter Daszak
- EcoHealth Alliance, 520 Eighth Avenue, Suite 1200, New York, NY, 10018, USA
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12
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Gao WH, Lin XD, Chen YM, Xie CG, Tan ZZ, Zhou JJ, Chen S, Holmes EC, Zhang YZ. Newly identified viral genomes in pangolins with fatal disease. Virus Evol 2020; 6:veaa020. [PMID: 32296543 PMCID: PMC7151644 DOI: 10.1093/ve/veaa020] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Epizootic pathogens pose a major threat to many wildlife species, particularly in the context of rapidly changing environments. Pangolins (order Pholidota) are highly threatened mammals, in large part due to the trade in illegal wildlife. During July to August 2018 four sick wild pangolins (three Manis javanica and one Manis pentadactyla) exhibiting a variety of clinical symptoms were rescued by the Jinhua Wildlife Protection Station in Zhejiang province, China. Although three of these animals died, fortunately one recovered after 2 weeks of symptomatic treatment. Using meta-transcriptomics combined with reverse transcription polymerase chain reaction (RT-PCR), we identified two novel RNA viruses in two of the dead pangolins. Genomic analysis revealed that these viruses were most closely related to pestiviruses and coltiviruses, although still highly genetically distinct, with more than 48 and 25 per cent sequence divergence at the amino acid level, respectively. We named these Dongyang pangolin virus (DYPV) and Lishui pangolin virus (LSPV) based on the sampling site and hosts. Although coltiviruses (LSPV) are known to be transmitted by ticks, we found no evidence of LSPV in ticks sampled close to where the pangolins were collected. In addition, although DYPV was present in nymph ticks (Amblyomma javanense) collected from a diseased pangolin, they were not found in the local tick population. Epidemiological investigation revealed that both novel viruses might have been imported following the illegal international trade of pangolins. Hence, these data indicate that illegal wildlife trafficking not only threatens the status of pangolin populations, but may also spread epizootic pathogens.
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Affiliation(s)
- Wen-Hua Gao
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xian-Dan Lin
- Wenzhou Center for Disease Control and Prevention, Wenzhou, 325001, Zhejiang, China
| | - Yan-Mei Chen
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Shanghai Public Health Clinical Center & School of Life Science, Fudan University, Shanghai, 201052, China
| | - Chun-Gang Xie
- Jinhua Wildlife Protection Station, Jinhua Forestry Bureau, Jinhua, 321000, Zhejiang, China
| | - Zhi-Zhou Tan
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jia-Jun Zhou
- Zhejiang Forest Resource Monitoring Center, Hangzhou, 310020, Zhejiang, China
| | - Shuai Chen
- Wenzhou Center for Disease Control and Prevention, Wenzhou, 325001, Zhejiang, China
| | - Edward C Holmes
- Shanghai Public Health Clinical Center & School of Life Science, Fudan University, Shanghai, 201052, China.,Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Yong-Zhen Zhang
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Shanghai Public Health Clinical Center & School of Life Science, Fudan University, Shanghai, 201052, China
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13
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Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins ( Manis javanica). Viruses 2019; 11:v11110979. [PMID: 31652964 PMCID: PMC6893680 DOI: 10.3390/v11110979] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022] Open
Abstract
Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.
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