1
|
Wang Y, Lin X, Li C, Liu G, Wang S, Chen M, Wei X, Wen H, Tao Z, Xu Y. Metagenomic sequencing reveals viral diversity of mosquitoes from Shandong Province, China. Microbiol Spectr 2024; 12:e0393223. [PMID: 38466099 DOI: 10.1128/spectrum.03932-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
Mosquitoes carry a large number of known and unknown viruses, some of which could cause serious diseases in humans or animals. Metagenomic sequencing for mosquito viromes is crucial for understanding the evolutionary history of viruses and preventing emerging mosquito-borne diseases. We collected 1,598 mosquitoes belonging to four species from five counties in Shandong Province, China in 2021. They were grouped by species and sampling locations and subjected to metagenomic next-generation sequencing for the analysis of the viromes. A total of 233,317,352 sequencing reads were classified into 30 viral families and an unclassified group. Comparative analysis showed that mosquitoes in Shandong Province generally possessed host-specific virome. We detected mosquito-borne viruses including Japanese encephalitis virus, Getah virus, and Kadipiro virus in Culex tritaeniorhynchus and Anopheles sinensis samples. Phylogenetic analysis showed that these pathogenic viruses may have existed in mosquitoes in Shandong Province for a long time. Meanwhile, we identified 22 novel viruses belonging to seven families and the genus Negevirus. Our study comprehensively described the viromes of several common mosquito species in Shandong Province, China, and demonstrated the major role of host species in shaping mosquito viromes. Furthermore, the metagenomic data provided valuable epidemiological information on multiple mosquito-borne viruses, highlighting the potential risk of infection transmission. IMPORTANCE Mosquitoes are known as the source of various pathogens for humans and animals. Culex tritaeniorhynchus, Armigeres subalbatus, and Anopheles sinensis have been found to transmit the Getah virus, which has recently caused increasing infections in China. Cx. tritaeniorhynchus and Culex pipiens are the main vectors of Japanese encephalitis virus and have caused epidemics of Japanese encephalitis in China in past decades. These mosquitoes are widely present in Shandong Province, China, leading to a great threat to public health and the breeding industry. This study provided a comprehensive insight into the viromes of several common mosquito species in Shandong Province, China. The metagenomic sequencing data revealed the risks of multiple pathogenic mosquito-borne viruses, including Japanese encephalitis virus, Getah virus, and Kadipiro virus, which are of great importance for preventing emerging viral epidemics.
Collapse
Affiliation(s)
- Yuhao Wang
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiaojuan Lin
- Division of EPI, Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Chao Li
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Guifang Liu
- Division of EPI, Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Suting Wang
- Division of EPI, Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Meng Chen
- Division of EPI, Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Xuemin Wei
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Hongling Wen
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Zexin Tao
- Division of EPI, Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Yifei Xu
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Suzhou Research Institute of Shandong University, Suzhou, Jiangsu, China
| |
Collapse
|
2
|
Munday JS, Dunbar ME, Wightman P, Piripi S. Osteoinductive squamous cell carcinoma associated with a putative novel papillomavirus on the digit of a cat. N Z Vet J 2024; 72:112-117. [PMID: 38043925 DOI: 10.1080/00480169.2023.2285294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/13/2023] [Indexed: 12/05/2023]
Abstract
CASE HISTORY AND CLINICAL FINDINGS An approximately 10-year-old, castrated male domestic short-haired cat developed swelling and ulceration of the second digit of the right front paw. Radiographs revealed a spherical soft tissue swelling with irregular distal margins that contained multiple lacy mineral opacities. The digit was amputated and submitted for histology. No recurrence has been observed 7 months after amputation. PATHOLOGICAL AND MOLECULAR FINDINGS Histology revealed a moderately well-circumscribed proliferation of well-differentiated squamous cells arranged in trabeculae and nests. Numerous thin spicules of osseous metaplasia were visible throughout the neoplasm. Around 70% of the neoplastic cells contained papillomavirus-induced cell changes including large amphophilic cytoplasmic bodies and cells with shrunken nuclei surrounded by a clear halo. Intense p16CDKN2A protein immunostaining was visible within the neoplastic cells, suggesting papillomavirus-induced changes in cell regulation. A DNA sequence from a putative novel Taupapillomavirus type was amplified from the neoplasm. DIAGNOSIS Osteoinductive squamous cell carcinoma associated with a putative novel papillomavirus type. CLINICAL RELEVANCE The findings in this case increase the number of papillomavirus types known to infect cats, and the squamous cell carcinoma had histological features that have not been previously reported. The neoplasm was not as invasive as is typical for a squamous cell carcinoma and excision appeared curative. This is the first report of an osteoinductive squamous cell carcinoma of the skin of cats and the neoplasm had a unique radiographic appearance.
Collapse
Affiliation(s)
- J S Munday
- Department of Pathobiology, Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - M E Dunbar
- Pet Doctors Hillcrest, Hamilton, New Zealand
| | - P Wightman
- Veterinary Teaching Hospital, Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - S Piripi
- IDEXX Laboratories (NZ), Palmerston North, New Zealand
| |
Collapse
|
3
|
Wang R, Liu S, Xu C, Yu J, Wei J, Ding W, Li Y. Identification and characterization of a novel Cytorhabdovirus associated with goji berry ( Lycium barbarum L.) crinkle disease. Front Microbiol 2024; 14:1294616. [PMID: 38239727 PMCID: PMC10794335 DOI: 10.3389/fmicb.2023.1294616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024] Open
Abstract
Goji berry (Lycium barbarum L.) is a traditional Chinese herbal medicinal plant that is extensively cultivated in the arid and semiarid regions of northwest China. In this study, a novel cytorhabdovirus, tentatively named "goji cytorhabdovirus A (GCVA)," was identified from the goji berry plant exhibiting leaf crinkle symptoms through high-throughput sequencing (HTS). GCVA contains a linear, negative sense single-stranded RNA genome of 14,812 nucleotides and encodes six open reading frames in the order of 3' leader-N-P-P4-M-G-L-5' trailer. The genome of GCVA shares the highest nucleotide (nt) identity of 65.80% (16% query coverage) with yerba mate virus A (YmVA) (NC_076472). The N and L proteins also share low amino acid (aa) identities (<35.42 and < 41.23%, respectively) with known cytorhabdoviruses. Typical features of the viruses in the genus Cytorhabdovirus include a highly conserved consensus sequence in the intergenic regions and extensive complementation of the 5' non-coding trailer and the 3' leader. These features were also found in GCVA. These data in combination with a phylogenetic analysis that was based on the aa sequences of the N and L proteins support the proposal that GCVA is a new species in the genus Cytorhabdovirus.
Collapse
Affiliation(s)
| | | | | | | | | | - Wanlong Ding
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
4
|
Walt HK, Kooienga E, Cammack JA, Tomberlin JK, Jordan HR, Meyer F, Hoffmann FG. Bioinformatic Surveillance Leads to Discovery of Two Novel Putative Bunyaviruses Associated with Black Soldier Fly. Viruses 2023; 15:1654. [PMID: 37631997 PMCID: PMC10460066 DOI: 10.3390/v15081654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
The black soldier fly (Hermetia illucens, BSF) has emerged as an industrial insect of high promise because of its ability to convert organic waste into nutritious feedstock, making it an environmentally sustainable alternative protein source. As global interest rises, rearing efforts have also been upscaled, which is highly conducive to pathogen transmission. Viral epidemics have stifled mass-rearing efforts of other insects of economic importance, such as crickets, silkworms, and honeybees, but little is known about the viruses that associate with BSF. Although BSFs are thought to be unusually resistant to pathogens because of their expansive antimicrobial gene repertoire, surveillance techniques could be useful in identifying emerging pathogens and common BSF microbes. In this study, we used high-throughput sequencing data to survey BSF larvae and frass samples, and we identified two novel bunyavirus-like sequences. Our phylogenetic analysis grouped one in the family Nairoviridae and the other with two unclassified bunyaviruses. We describe these putative novel viruses as BSF Nairovirus-like 1 and BSF uncharacterized bunyavirus-like 1. We identified candidate segments for the full BSF Nairovirus-like 1 genome using a technique based on transcript co-occurrence and only a partial genome for BSF uncharacterized bunyavirus-like 1. These results emphasize the value of routine BSF colony surveillance and add to the number of viruses associated with BSF.
Collapse
Affiliation(s)
- Hunter K. Walt
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA;
| | - Emilia Kooienga
- Department of Biology, Mississippi State University, Starkville, MS 39762, USA (H.R.J.)
| | - Jonathan A. Cammack
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.A.C.); (J.K.T.)
- EVO Conversion Systems, LLC, College Station, TX 77845, USA
| | - Jeffery K. Tomberlin
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.A.C.); (J.K.T.)
| | - Heather R. Jordan
- Department of Biology, Mississippi State University, Starkville, MS 39762, USA (H.R.J.)
| | - Florencia Meyer
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA;
| | - Federico G. Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA;
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39762, USA
| |
Collapse
|
5
|
Diaz-Lara A, Stevens K, Aguilar-Molina VH, Fernández-Cortés JM, Chabacano León VM, De Donato M, Sharma A, Erickson TM, Al Rwahnih M. High-Throughput Sequencing of Grapevine in Mexico Reveals a High Incidence of Viruses including a New Member of the Genus Enamovirus. Viruses 2023; 15:1561. [PMID: 37515247 PMCID: PMC10386000 DOI: 10.3390/v15071561] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/08/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
This is the first viral metagenomic analysis of grapevine conducted in Mexico. During the summer of 2021, 48 plants displaying virus-like symptoms were sampled in Queretaro, an important grapevine-producing area of Mexico, and analyzed for the presence of viruses via high-throughput sequencing (HTS). The results of HTS were verified by real-time RT-PCR following a standardized testing scheme (Protocol 2010). Fourteen different viruses were identified, including grapevine asteroid mosaic-associated virus (GAMaV), grapevine Cabernet Sauvignon reovirus (GCSV), grapevine fanleaf virus (GFLV), grapevine fleck virus (GFkV), grapevine Pinot gris virus (GPGV), grapevine red globe virus (GRGV), grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine rupestris vein feathering virus (GRVFV), grapevine Syrah virus 1 (GSyV-1), grapevine virus B (GVB), and grapevine leafroll-associated viruses 1, 2, 3, 4 (GLRaV1, 2, 3, 4). Additionally, divergent variants of GLRaV4 and GFkV, and a novel Enamovirus-like virus were discovered. This is the first report of GAMaV, GCSV, GLRaV4, GPGV, GRGV, GRVFV, and GSyV-1 infecting grapevines in Mexico; the impact of these pathogens on production is unknown.
Collapse
Affiliation(s)
- Alfredo Diaz-Lara
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Kristian Stevens
- Departments of Computer Science and Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
| | | | | | | | - Marcos De Donato
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Ashutosh Sharma
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Teresa M Erickson
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
| | - Maher Al Rwahnih
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
| |
Collapse
|
6
|
Munday JS, Grant K, Orbell G, Vaatstra BL. Cutaneous plaques associated with a putative novel papillomavirus type in a horse. N Z Vet J 2023; 71:100-105. [PMID: 36484093 DOI: 10.1080/00480169.2022.2157347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
CASE HISTORY AND CLINICAL FINDINGS A 6-year-old Thoroughbred mare developed multiple flat plaques, < 1 cm in diameter, on the left front fetlock. These were treated topically using 5-fluorouracil and resolved after 4 weeks. However, additional similar plaques developed on the left front pastern 5 months later. These lesions resolved within 3 months without treatment. PATHOLOGICAL AND MOLECULAR FINDINGS One plaque that developed initially and one plaque that developed later were examined histologically. Both consisted of well-demarcated foci of moderate epidermal hyperplasia. Scattered throughout both plaques were cells showing evidence of papillomavirus-induced cell changes and the same papillomaviral DNA sequence was amplified from both lesions using PCR. As the novel sequence had 79.1% similarity to a partial sequence previously amplified from an equine cutaneous wart and 67.9% similarity to Equus caballus papillomavirus type 1, these results indicate detection of a putative novel papillomavirus type. DIAGNOSIS Multiple cutaneous plaques due to infection by a novel papillomavirus type. CLINICAL RELEVANCE Unlike more typical equine cutaneous warts which generally appear as pedunculated and filiform masses, the lesions in this horse appeared as raised plaques. With the exception of aural plaques that are confined to the ears, localised clusters of papillomaviral plaques have not been previously described in horses. The lesions contained subtle histological evidence of papillomavirus infection and careful examination is required to differentiate these plaques from pre-neoplastic lesions. The plaques contained a putative novel papillomavirus type. These results increase the spectrum of papillomavirus-induced skin disease in horses.
Collapse
Affiliation(s)
- J S Munday
- Department of Pathobiology, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - K Grant
- South Wairarapa Veterinary Services, Carterton, New Zealand
| | - G Orbell
- Gribbles Veterinary Ltd, Palmerston North, New Zealand
| | - B L Vaatstra
- Gribbles Veterinary Ltd, Palmerston North, New Zealand
| |
Collapse
|
7
|
Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. Life (Basel) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
Collapse
Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
| |
Collapse
|
8
|
Ozeki T, Abe H, Ushijima Y, Nze-Nkogue C, Akomo-Okoue EF, Ella GWE, Koumba LBM, Nso BCBB, Mintsa-Nguema R, Makouloutou-Nzassi P, Makanga BK, Nguelet FLM, Ondo GN, Mbadinga MJVM, Igasaki Y, Okada S, Hirano M, Yoshii K, Lell B, Bonney LC, Hewson R, Kurosaki Y, Yasuda J. Identification of novel orthonairoviruses from rodents and shrews in Gabon, Central Africa. J Gen Virol 2022; 103. [PMID: 36215163 DOI: 10.1099/jgv.0.001796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Africa, several emerging zoonotic viruses have been transmitted from small mammals such as rodents and shrews to humans. Although no clinical cases of small mammal-borne viral diseases have been reported in Central Africa, potential zoonotic viruses have been identified in rodents in the region. Therefore, we hypothesized that there may be unrecognized zoonotic viruses circulating in small mammals in Central Africa. Here, we investigated viruses that have been maintained among wild small mammals in Gabon to understand their potential risks to humans. We identified novel orthonairoviruses in 24.6 % of captured rodents and shrews from their kidney total RNA samples. Phylogenetic analysis revealed that the novel viruses, Lamusara virus (LMSV) and Lamgora virus, were closely related to Erve virus, which was previously identified in shrews of the genus Crocidura and has been suspected to cause neuropathogenic diseases in humans. Moreover, we show that the LMSV ovarian tumour domain protease, one of the virulence determination factors of orthonairoviruses, suppressed interferon signalling in human cells, suggesting the possible human pathogenicity of this virus. Taken together, our study demonstrates the presence of novel orthonairoviruses that may pose unrecognized risks of viral disease transmission in Gabon.
Collapse
Affiliation(s)
- Takehiro Ozeki
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan.,Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan
| | - Yuri Ushijima
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
| | - Chimène Nze-Nkogue
- Institut de Recherche en Ecologie Tropicale (IRET), Libreville BP13354, Gabon
| | | | - Ghislain W E Ella
- Institut de Recherche en Ecologie Tropicale (IRET), Libreville BP13354, Gabon
| | - Lilian B M Koumba
- Institut de Recherche en Ecologie Tropicale (IRET), Libreville BP13354, Gabon
| | - Branly C B B Nso
- Institut de Recherche en Ecologie Tropicale (IRET), Libreville BP13354, Gabon
| | | | | | - Boris K Makanga
- Institut de Recherche en Ecologie Tropicale (IRET), Libreville BP13354, Gabon
| | - Fred L M Nguelet
- Institut de Recherche en Ecologie Tropicale (IRET), Libreville BP13354, Gabon
| | - Georgelin N Ondo
- Centre de Recherche Médicales de Lambaréné (CERMEL), Lambaréné BP242, Gabon
| | | | - Yui Igasaki
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
| | - Sayaka Okada
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan
| | - Minato Hirano
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan
| | - Kentaro Yoshii
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan
| | - Bertrand Lell
- Centre de Recherche Médicales de Lambaréné (CERMEL), Lambaréné BP242, Gabon.,University of Tübingen, Tübingen 72072, Germany.,Medical University of Vienna, Vienna 1090, Austria
| | - Laura C Bonney
- United Kingdom Health Security Agency (UKHSA), Porton Down, Salisbury SP4 0JZ, UK
| | - Roger Hewson
- United Kingdom Health Security Agency (UKHSA), Porton Down, Salisbury SP4 0JZ, UK
| | - Yohei Kurosaki
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan.,Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan
| |
Collapse
|
9
|
Madera S, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, DeRisi JL, Aguilar HC, Lacoste V, Dussart P, Heraud JM, Brook CE. Discovery and Genomic Characterization of a Novel Henipavirus, Angavokely Virus, from Fruit Bats in Madagascar. J Virol 2022; 96:e0092122. [PMID: 36040175 DOI: 10.1128/jvi.00921-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Henipavirus (family Paramyxoviridae) currently comprises seven viruses, four of which have demonstrated prior evidence of zoonotic capacity. These include the biosafety level 4 agents Hendra (HeV) and Nipah (NiV) viruses, which circulate naturally in pteropodid fruit bats. Here, we describe and characterize Angavokely virus (AngV), a divergent henipavirus identified in urine samples from wild, Madagascar fruit bats. We report the nearly complete 16,740-nucleotide genome of AngV, which encodes the six major henipavirus structural proteins (nucleocapsid, phosphoprotein, matrix, fusion, glycoprotein, and L polymerase). Within the phosphoprotein (P) gene, we identify an alternative start codon encoding the AngV C protein and a putative mRNA editing site where the insertion of one or two guanine residues encodes, respectively, additional V and W proteins. In other paramyxovirus systems, C, V, and W are accessory proteins involved in antagonism of host immune responses during infection. Phylogenetic analysis suggests that AngV is ancestral to all four previously described bat henipaviruses-HeV, NiV, Cedar virus (CedV), and Ghanaian bat virus (GhV)-but evolved more recently than rodent- and shrew-derived henipaviruses, Mojiang (MojV), Gamak (GAKV), and Daeryong (DARV) viruses. Predictive structure-based alignments suggest that AngV is unlikely to bind ephrin receptors, which mediate cell entry for all other known bat henipaviruses. Identification of the AngV receptor is needed to clarify the virus's potential host range. The presence of V and W proteins in the AngV genome suggest that the virus could be pathogenic following zoonotic spillover. IMPORTANCE Henipaviruses include highly pathogenic emerging zoonotic viruses, derived from bat, rodent, and shrew reservoirs. Bat-borne Hendra (HeV) and Nipah (NiV) are the most well-known henipaviruses, for which no effective antivirals or vaccines for humans have been described. Here, we report the discovery and characterization of a novel henipavirus, Angavokely virus (AngV), isolated from wild fruit bats in Madagascar. Genomic characterization of AngV reveals all major features associated with pathogenicity in other henipaviruses, suggesting that AngV could be pathogenic following spillover to human hosts. Our work suggests that AngV is an ancestral bat henipavirus that likely uses viral entry pathways distinct from those previously described for HeV and NiV. In Madagascar, bats are consumed as a source of human food, presenting opportunities for cross-species transmission. Characterization of novel henipaviruses and documentation of their pathogenic and zoonotic potential are essential to predicting and preventing the emergence of future zoonoses that cause pandemics.
Collapse
|
10
|
Zheng L, Fu S, Xie Y, Han Y, Zhou X, Wu J. Discovery and Characterization of a Novel Umbravirus from Paederia scandens Plants Showing Leaf Chlorosis and Yellowing Symptoms. Viruses 2022; 14:v14081821. [PMID: 36016443 PMCID: PMC9414234 DOI: 10.3390/v14081821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/13/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Umbraviruses are a special class of plant viruses that do not encode any viral structural proteins. Here, a novel umbravirus that has been tentatively named Paederia scandens chlorosis yellow virus (PSCYV) was discovered through RNA-seq in Paederia scandens plants showing leaf chlorosis and yellowing symptoms. The PSCYV genome is a 4301 nt positive-sense, single strand RNA that contains four open reading frames (ORFs), i.e., ORF1–4, that encode P1–P4 proteins, respectively. Together, ORF1 and ORF2 are predicted to encode an additional protein, RdRp, through a −1 frameshift mechanism. The P3 protein encoded by ORF3 was predicted to be the viral long-distance movement protein. P4 was determined to function as the viral cell-to-cell movement protein (MP) and transcriptional gene silencing (TGS) suppressor. Both P1 and RdRp function as weak post-transcriptional gene silencing (PTGS) suppressors of PSCYV. The PVX-expression system indicated that all viral proteins may be symptom determinants of PSCYV. Phylogenetic analysis indicated that PSCYV is evolutionarily related to members of the genus Umbravirus in the family Tombusviridae. Furthermore, a cDNA infectious clone of PSCYV was successfully constructed and used to prove that PSCYV can infect both Paederia scandens and Nicotiana benthamiana plants through mechanical inoculation, causing leaf chlorosis and yellowing symptoms. These findings have broadened our understanding of umbraviruses and their host range.
Collapse
Affiliation(s)
- Lianshun Zheng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Shuai Fu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yi Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yang Han
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (X.Z.); (J.W.); Tel.: +86-571-88982250 (J.W.)
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
- Correspondence: (X.Z.); (J.W.); Tel.: +86-571-88982250 (J.W.)
| |
Collapse
|
11
|
Shvets D, Porotikova E, Sandomirsky K, Vinogradova S. Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia). Viruses 2022; 14:1314. [PMID: 35746784 DOI: 10.3390/v14061314] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
Grapevine germplasm collections are unique repositories of grape cultivars; therefore, it is necessary to minimize their infection with pathogens, including viruses, and develop various programs to maintain them in a virus-free state. In our study, we examined the virome of the largest Russian grapevine germplasm collection, the Anapa Ampelographic Collection, using high-throughput sequencing of total RNAs. As a result of bioinformatics analysis and validation of its results by reverse transcription PCR (RT-PCR) and quantitative RT-PCR (RT-qPCR), we identified 20 viruses and 3 viroids in 47 libraries. All samples were infected with 2 to 12 viruses and viroids, including those that cause economically significant diseases: leafroll, fleck, and rugose wood complex. For the first time in Russia, we detected Grapevine virus B (GVB), Grapevine virus F (GVF), Grapevine asteroid mosaic-associated virus (GAMaV), Grapevine Red Globe virus (GRGV), Grapevine satellite virus (GV-Sat), Grapevine virga-like virus (GVLV), Grapevine-associated jivivirus 1 (GaJV-1) and Vitis cryptic virus (VCV). A new putative representative of the genus Umbravirus with the provisional name Grapevine umbra-like virus (GULV) was also identified in Russian grape samples.
Collapse
|
12
|
Abstract
Obesity has been linked to higher morbidity and mortality in those that contract novel viruses, such as H1N1 and SARS-CoV-2. Loss of life and the high cost of obesity highlight the need to focus on preventative measures. The state of Maine (United States) is profiled as a rural state with high rates of obesity and low health literacy that benefits from programs to improve health. However, more multidirectional efforts are needed. Four recommendations for building a healthier, more resilient patient population are discussed here: (i) state incentives and subsidies, (ii) employers to incentivize healthy living, (iii) federal incentives and initiatives, and (iv) personal responsibility for health and wellness.
Collapse
|
13
|
Koloniuk I, Přibylová J, Čmejla R, Valentová L, Fránová J. Identification and Characterization of a Novel Umbra-like Virus, Strawberry Virus A, Infecting Strawberry Plants. Plants (Basel) 2022; 11:plants11050643. [PMID: 35270113 PMCID: PMC8912295 DOI: 10.3390/plants11050643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/23/2022] [Accepted: 02/23/2022] [Indexed: 05/08/2023]
Abstract
A novel RNA virus infecting strawberry plants was discovered using high-throughput sequencing. The analyzed plant was simultaneously infected with three different genetic variants of the virus, provisionally named strawberry virus A (StrVA). Although StrVA is phylogenetically clustered with several recently discovered, unclassified plant viruses, it has a smaller genome and several unique features in its genomic organization. A specific and sensitive qPCR system for the detection of identified StrVA genetic variants was designed. A survey conducted in the Czech Republic revealed that StrVA was present in 28.3% of strawberry samples (n = 651) from various origins (plantations, gardens, and propagation material). Sequencing of 48 randomly selected StrVA-positive strawberry samples showed that two or all three StrVA genetic variants were present in 62.5% of the samples in various proportions. StrVA was found in mixed infections with other viruses (strawberry mild yellow edge virus, strawberry crinkle virus, strawberry mottle virus, strawberry polerovirus 1, or strawberry virus 1) in 57.1% of the samples, which complicated the estimation of its biological relevance and impact on the health status of the plants.
Collapse
Affiliation(s)
- Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 České Budějovice, Czech Republic; (J.P.); (J.F.)
- Correspondence: ; Tel.: +420-38-777-5521
| | - Jaroslava Přibylová
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 České Budějovice, Czech Republic; (J.P.); (J.F.)
| | - Radek Čmejla
- Research & Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, 508 01 Horice, Czech Republic; (R.Č.); (L.V.)
| | - Lucie Valentová
- Research & Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, 508 01 Horice, Czech Republic; (R.Č.); (L.V.)
| | - Jana Fránová
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 České Budějovice, Czech Republic; (J.P.); (J.F.)
| |
Collapse
|
14
|
Zhang C, Burch M, Wylie K, Herter B, Franklin CL, Ericsson AC. Characterization of the Eukaryotic Virome of Mice from Different Sources. Microorganisms 2021; 9:microorganisms9102064. [PMID: 34683385 PMCID: PMC8538372 DOI: 10.3390/microorganisms9102064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
Accumulating studies show that the host microbiome influences the development or progression of many diseases. The eukaryotic virome, as a key component of the microbiome, plays an important role in host health and disease in humans and animals, including research animals designed to model human disease. To date, the majority of research on the microbiome has focused on bacterial populations, while less attention has been paid to the viral component. Members of the eukaryotic virome interact with the commensal bacterial microbiome through trans-kingdom interactions, and influence host immunity and disease phenotypes as a collective microbial ecosystem. As such, differences in the virome may affect the reproducibility of animal models, and supplementation of the virome may enhance the translatability of animal models of human disease. However, there are minimal empirical data regarding differences in the virome of mice from different commercial sources. Our hypotheses were that the mice obtained from pet store sources and lab mice differ in their eukaryotic virome, and that lab mice from different sources would also have different viromes. To test this hypothesis, the ViroCap platform was used to characterize the eukaryotic virome in multiple tissues of mice from different sources including three sources of laboratory mice and two pet stores. As expected, pet store mice harbored a much greater diversity within the virome compared to lab mice. This included an ostensibly novel norovirus strain identified in one source of these mice. Viruses found in both laboratory and pet store populations included four strains of endogenous retroviruses and murine astrovirus with the latter being restricted to one source of lab mice. Considering the relatively high richness virome within different samples from healthy humans, these data suggest that mouse models from alternative sources may be more translational to the human condition. Moreover, these data demonstrate that, by characterizing the eukaryotic murine virome from different sources, novel viruses may be identified for use as field strains in biomedical research.
Collapse
Affiliation(s)
- Chunye Zhang
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (C.Z.); (M.B.)
| | - Matt Burch
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (C.Z.); (M.B.)
| | - Kristine Wylie
- Department of Pediatrics, Washington University, St. Louis, MO 63110, USA; (K.W.); (B.H.)
- McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Brandi Herter
- Department of Pediatrics, Washington University, St. Louis, MO 63110, USA; (K.W.); (B.H.)
| | - Craig L. Franklin
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (C.Z.); (M.B.)
- Metagenomics Center, University of Missouri, Columbia, MO 65201, USA
- Mutant Mouse Resource and Research Center, University of Missouri, Columbia, MO 65201, USA
- Correspondence: (C.L.F.); (A.C.E.)
| | - Aaron C. Ericsson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (C.Z.); (M.B.)
- Metagenomics Center, University of Missouri, Columbia, MO 65201, USA
- Mutant Mouse Resource and Research Center, University of Missouri, Columbia, MO 65201, USA
- Correspondence: (C.L.F.); (A.C.E.)
| |
Collapse
|
15
|
Liu L, Shen Q, Li N, He Y, Han N, Wang X, Meng J, Peng Y, Pan M, Jin Y, Jiang T, Tan W, Wang J, Wu A. Comparative viromes of Culicoides and mosquitoes reveal their consistency and diversity in viral profiles. Brief Bioinform 2020; 22:6032619. [PMID: 33313676 DOI: 10.1093/bib/bbaa323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/25/2022] Open
Abstract
The genus Culicoides includes biting midges, some of which are vectors for viruses that cause diseases in humans and animals. Knowledge of the roles of Culicoides in viral ecology is inadequate. We collected ~300 000 samples of Culicoides and mosquitoes in 15 representative regions within Yunnan, China. Using mosquitoes as reference vectors, we designed a comparative virome strategy to study the viral composition, diversity, hosts and spatiotemporal distribution of Culicoides. A map of viromes in Culicoides and mosquitoes in Yunan province, China, was constructed. At the same locations, Culicoides and mosquitoes usually share a similar viral diversity. At least 10 important pathogenic viruses were detected from Culicoides. Many novel viruses were discovered, including 21 segmented viruses of Flaviviridae, 180 viruses of Monjiviricetes and 130 viruses of Bunyavirales. The findings demonstrate that Culicoides is an important part of viral ecology and should be studied and monitored for potentially emerging viruses.
Collapse
Affiliation(s)
- Lin Liu
- Suzhou Institute of Systems Medicine
| | - Qin Shen
- Suzhou Institute of Systems Medicine
| | - Nan Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory,Yunnan Animal Science and Veterinary Institute
| | - Yuwen He
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory,Yunnan Animal Science and Veterinary Institute
| | - Na Han
- Suzhou Institute of Systems Medicine
| | | | - Jinxin Meng
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory,Yunnan Animal Science and Veterinary Institute
| | | | - Mei Pan
- lab masters in the high-throughput sequencing platform of the Suzhou Institute of Systems Medicine
| | - Yuting Jin
- lab masters in the high-throughput sequencing platform of the Suzhou Institute of Systems Medicine
| | | | - Wenjie Tan
- National Institute for Viral Disease Control and Prevention, China CDC
| | | | - Aiping Wu
- Suzhou Institute of Systems Medicine
| |
Collapse
|
16
|
Abstract
COVID-19 has grown into a global pandemic that has strained healthcare throughout the world. There is a sense of urgency in finding a cure for this deadly virus. In this study, we reviewed the empiric options used in common practice for COVID-19, based on the literature available online, with an emphasis on human experiences with these treatments on severe acute respiratory syndrome-associated coronavirus (SARS-COV-1) and other viruses. Convalescent blood products are the most promising potential treatment for use in COVID-19. The use of chloroquine or hydroxychloroquine (HCQ), remdesivir, and tocilizumab are some of the other promising potential therapies; however, they are yet to be tested in randomized clinical trials (RCTs). The use of lopinavir-ritonavir did not prove beneficial in a large RCT. The use of corticosteroids should be avoided in COVID-19 pneumonia unless used for other indications, based on the suggestion of harm in patients with SARS-COV-1 and Middle Eastern Respiratory Syndrome (MERS) infection. The reviews of this paper are available via the supplemental material section.
Collapse
Affiliation(s)
- Muhammad Hamdan Gul
- Internal Medicine Department, Amita-Presence Saint Joseph Hospital, Chicago, 2900 N Lakeshore Drive, Chicago, IL 60657, USA
| | - Zin Mar Htun
- Internal Medicine Department, Louis A Weiss Memorial Hospital, Chicago, IL, USA
| | - Nauman Shaukat
- Cardiothoracic Surgery, Saint George’s University Hospital, Tooting, London, UK
| | - Muhammad Imran
- Cardiothoracic Surgery, Armed Forces Institute, Rawalpindi, Pakistan
| | - Ahmad Khan
- Internal Medicine Department, West Virginia University- Charleston Division, WV, USA
| |
Collapse
|
17
|
Du J, Wang W, Chan JFW, Wang G, Huang Y, Yi Y, Zhu Z, Peng R, Hu X, Wu Y, Zeng J, Zheng J, Cui X, Niu L, Zhao W, Lu G, Yuen KY, Yin F. Identification of a Novel Ichthyic Parvovirus in Marine Species in Hainan Island, China. Front Microbiol 2019; 10:2815. [PMID: 31866980 PMCID: PMC6907010 DOI: 10.3389/fmicb.2019.02815] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/20/2019] [Indexed: 01/27/2023] Open
Abstract
Parvoviruses are a diverse group of viruses that are capable of infecting a wide range of animals. In this study, we report the discovery of a novel parvovirus, tilapia parvovirus HMU-HKU, in the fecal samples of crocodiles and intestines of tilapia in Hainan Province, China. The novel parvovirus was firstly identified from crocodiles fed with tilapia using next-generation sequencing (NGS). Screening studies revealed that the prevalence of the novel parvovirus in crocodile feces samples fed on tilapia (75–86%) was apparently higher than that in crocodiles fed with chicken (4%). Further studies revealed that the prevalence of the novel parvovirus in tilapia feces samples collected at four areas in Hainan Province was between 40 and 90%. Four stains of the novel parvovirus were identified in this study based on sequence analyses of NS1 and all the four strains were found in tilapia in contrast only two of them were detected in crocodile feces. The nearly full-length genome sequence of the tilapia parvovirus HMU-HKU-1 was determined and showed less than 45.50 and 40.38% amino acid identity with other members of Parvoviridae in NS1 and VP1 genes, respectively. Phylogenetic analysis based on the complete helicase domain amino acid sequences showed that the tilapia parvovirus HMU-HKU-1 formed a relatively independent branch in the newly proposed genus Chaphamaparvovirus in the subfamily Hamaparvovirinae according to the ICTV’s most recent taxonomic criteria for Parvoviridae classification. Tilapia parvovirus HMU-HKU-1 likely represented a new species within the new genus Chaphamaparvovirus. The identification of tilapia parvovirus HMU-HKU provides further insight into the viral and genetic diversity of parvoviruses and its infections in tilapia populations need to be evaluated in terms of pathogenicity and production losses in tilapia farming.
Collapse
Affiliation(s)
- Jiang Du
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Wenqi Wang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Jasper Fuk-Woo Chan
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Gaoyu Wang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yi Huang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yufang Yi
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Zheng Zhu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ruoyan Peng
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Xiaoyuan Hu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yue Wu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Jifeng Zeng
- Key Laboratory of Tropical Animal Breeding and Epidemic Disease Research of Hainan Province, Hainan University, Haikou, China.,Key Laboratory of Tropical Biological Resources of Ministry of Education, Haikou, China
| | - Jiping Zheng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xiuji Cui
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Lina Niu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Wei Zhao
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Gang Lu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Kwok-Yung Yuen
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Feifei Yin
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| |
Collapse
|
18
|
Dayaram A, Tsangaras K, Pavulraj S, Azab W, Groenke N, Wibbelt G, Sicks F, Osterrieder N, Greenwood AD. Novel Divergent Polar Bear-Associated Mastadenovirus Recovered from a Deceased Juvenile Polar Bear. mSphere 2018; 3:e00171-18. [PMID: 30045965 DOI: 10.1128/mSphere.00171-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cross-species transmission of viral pathogens is becoming an increasing problem for captive-animal facilities. This study highlights how animals in captivity are vulnerable to novel opportunistic pathogens, many of which do not result in straightforward diagnosis from symptoms and histopathology. In this study, a novel pathogen was suspected to have contributed to the death of a juvenile polar bear. HTS techniques were employed, and a novel Mastadenovirus was isolated. The virus was present in both the tissue and blood samples. Phylogenetic analysis of the virus at both the gene and genome levels revealed that it is highly divergent to other known mastadenoviruses. Overall, this study shows that animals in isolated conditions still come into contact with novel pathogens, and for many of these pathogens, the host reservoir and mode of transmission are yet to be determined. Polar bears in captivity can be exposed to opportunistic pathogens not present in their natural environments. A 4-month-old polar bear (Ursus maritimus) living in an isolated enclosure with his mother in the Tierpark Berlin, Berlin, Germany, was suffering from severe abdominal pain, mild diarrhea, and loss of appetite and died in early 2017. Histopathology revealed severe hepatic degeneration and necrosis without evidence of inflammation or inclusion bodies, although a viral infection had been suspected on the basis of the clinical signs. We searched for nucleic acids of pathogens by shotgun high-throughput sequencing (HTS) from genomic DNA and cDNA extracted from tissue and blood. We identified a novel Mastadenovirus and assembled a nearly complete genome from the shotgun sequences. Quantitative PCR (qPCR) revealed that viral DNA was present in various concentrations in all tissues examined and that the highest concentrations were found in blood. Viral culture did not yield cytopathic effects, but qPCR suggested that virus replication was sustained for up to three passages. Positive immunofluorescence staining confirmed that the virus was able to replicate in the cells during early passage. Phylogenetic analysis demonstrated that the virus is highly divergent compared to other previously identified Mastadenovirus members and basal to most known viral clades. The virus was found only in the 4-month-old bear and not in other captive polar bears tested. We surmised, therefore, that the polar bear was infected from an unknown reservoir, illustrating that adenoviral diversity remains underestimated and that cross-species transmission of viruses can occur even under conditions of relative isolation. IMPORTANCE Cross-species transmission of viral pathogens is becoming an increasing problem for captive-animal facilities. This study highlights how animals in captivity are vulnerable to novel opportunistic pathogens, many of which do not result in straightforward diagnosis from symptoms and histopathology. In this study, a novel pathogen was suspected to have contributed to the death of a juvenile polar bear. HTS techniques were employed, and a novel Mastadenovirus was isolated. The virus was present in both the tissue and blood samples. Phylogenetic analysis of the virus at both the gene and genome levels revealed that it is highly divergent to other known mastadenoviruses. Overall, this study shows that animals in isolated conditions still come into contact with novel pathogens, and for many of these pathogens, the host reservoir and mode of transmission are yet to be determined.
Collapse
|
19
|
Zhu W, Zhang H, Xiang X, Zhong L, Yang L, Guo J, Xie Y, Li F, Deng Z, Feng H, Huang Y, Hu S, Xu X, Zou X, Li X, Bai T, Chen Y, Li Z, Li J, Shu Y. Reassortant Eurasian Avian-Like Influenza A(H1N1) Virus from a Severely Ill Child, Hunan Province, China, 2015. Emerg Infect Dis 2018; 22:1930-1936. [PMID: 27767007 PMCID: PMC5088044 DOI: 10.3201/eid2211.160181] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Infectivity and virulence of this virus in mice are higher than for previous human-origin Eurasian avian–like viruses. In 2015, a novel influenza A(H1N1) virus was isolated from a boy in China who had severe pneumonia. The virus was a genetic reassortant of Eurasian avian-like influenza A(H1N1) (EA-H1N1) virus. The hemagglutinin, neuraminidase, and matrix genes of the reassortant virus were highly similar to genes in EA-H1N1 swine influenza viruses, the polybasic 1 and 2, polymerase acidic, and nucleoprotein genes originated from influenza A(H1N1)pdm09 virus, and the nonstructural protein gene derived from classical swine influenza A(H1N1) (CS H1N1) virus. In a mouse model, the reassortant virus, termed influenza A/Hunan/42443/2015(H1N1) virus, showed higher infectivity and virulence than another human EA-H1N1 isolate, influenza A/Jiangsu/1/2011(H1N1) virus. In the respiratory tract of mice, virus replication by influenza A/Hunan/42443/2015(H1N1) virus was substantially higher than that by influenza A/Jiangsu/1/2011(H1N1) virus. Human-to-human transmission of influenza A/Hunan/42443/2015(H1N1) virus has not been detected; however, given the circulation of novel EA-H1N1 viruses in pigs, enhanced surveillance should be instituted among swine and humans.
Collapse
MESH Headings
- Animals
- Cell Line
- China/epidemiology
- Genes, Viral
- History, 21st Century
- Humans
- Infant
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza, Human/diagnosis
- Influenza, Human/epidemiology
- Influenza, Human/history
- Influenza, Human/virology
- Multilocus Sequence Typing
- Phylogeny
- RNA, Viral
- Reassortant Viruses
- Serologic Tests
- Severity of Illness Index
- Virulence
- Virus Replication
Collapse
|
20
|
Frey KG, Biser T, Hamilton T, Santos CJ, Pimentel G, Mokashi VP, Bishop-Lilly KA. Bioinformatic Characterization of Mosquito Viromes within the Eastern United States and Puerto Rico: Discovery of Novel Viruses. Evol Bioinform Online 2016; 12:1-12. [PMID: 27346944 PMCID: PMC4912310 DOI: 10.4137/ebo.s38518] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/01/2016] [Accepted: 05/01/2016] [Indexed: 12/14/2022] Open
Abstract
Mosquitoes are efficient, militarily relevant vectors of infectious disease pathogens, including many RNA viruses. The vast majority of all viruses are thought to be undiscovered. Accordingly, recent studies have shown that viruses discovered in insects are very divergent from known pathogens and that many of them lack appropriate reference sequences in the public databases. Given that the majority of viruses are likely still undiscovered, environ mental sampling stands to provide much needed reference samples as well as genetic sequences for comparison. In this study, we sought to determine whether samples of mosquitoes collected from different sites (the Caribbean and locations on the US East Coast) could be differentiated using metagenomic analysis of the RNA viral fraction. We report here distinct virome profiles, even from samples collected short distances apart. In addition to profiling the previously known viruses from these samples, we detected a number of viruses that have been previously undiscovered.
Collapse
Affiliation(s)
- Kenneth G Frey
- Naval Medical Research Center - Frederick, Fort Detrick, MD, USA.; Henry M. Jackson Foundation, Bethesda, MD, USA
| | - Tara Biser
- Naval Medical Research Center - Frederick, Fort Detrick, MD, USA.; Hood College, Frederick, MD, USA
| | - Theron Hamilton
- Naval Medical Research Center - Frederick, Fort Detrick, MD, USA
| | | | | | | | - Kimberly A Bishop-Lilly
- Naval Medical Research Center - Frederick, Fort Detrick, MD, USA.; Henry M. Jackson Foundation, Bethesda, MD, USA
| |
Collapse
|
21
|
Oude Munnink BB, Cotten M, Canuti M, Deijs M, Jebbink MF, van Hemert FJ, Phan MVT, Bakker M, Jazaeri Farsani SM, Kellam P, van der Hoek L. A Novel Astrovirus-Like RNA Virus Detected in Human Stool. Virus Evol 2016; 2:vew005. [PMID: 27774298 PMCID: PMC4989881 DOI: 10.1093/ve/vew005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Several novel clades of astroviruses have recently been identified in human faecal samples. Here, we describe a novel astrovirus-like RNA virus detected in human stools, which we have tentatively named bastrovirus. The genome of this novel virus consists of 6,300 nucleotides organized in three open reading frames. Several sequence divergent strains were detected sharing 67–93 per cent nucleotide identity. Bastrovirus encodes a putative structural protein that is homologous to the capsid protein found in members of the Astroviridae family (45% amino acid identity). The virus also encodes a putative non-structural protein that is genetically distant from astroviruses but shares some homology to the non-structural protein encoded by members of the Hepeviridae family (28% amino acid identity). This novel bastrovirus is present in 8.7 per cent (35/400) of faecal samples collected from 300 HIV-1-positive and 100 HIV-1-negative individuals suggesting common occurrence of the virus. However, whether the source of the virus is infected human cells or other, for example, dietary, remains to be determined.
Collapse
Affiliation(s)
- Bas B. Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK and
| | - Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Maarten F. Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Formijn J. van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - My V. T. Phan
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK and
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Seyed Mohammad Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK and
- Division of Infection and Immunity, University College London, WC1E 6BT London, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
- *Corresponding author: E-mail:
| |
Collapse
|
22
|
Wu Z, Yang L, Yang F, Ren X, Jiang J, Dong J, Sun L, Zhu Y, Zhou H, Jin Q. Novel Henipa-like virus, Mojiang Paramyxovirus, in rats, China, 2012. Emerg Infect Dis 2015; 20:1064-6. [PMID: 24865545 PMCID: PMC4036791 DOI: 10.3201/eid2006.131022] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
23
|
Granzow H, Fichtner D, Schütze H, Lenk M, Dresenkamp B, Nieper H, Mettenleiter TC. Isolation and partial characterization of a novel virus from different carp species suffering gill necrosis - ultrastructure and morphogenesis. J Fish Dis 2014; 37:559-569. [PMID: 23865968 DOI: 10.1111/jfd.12150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/04/2013] [Accepted: 06/06/2013] [Indexed: 06/02/2023]
Abstract
Two isolates of a novel enveloped RNA virus were obtained from carp and koi carp with gill necrosis. Both isolates behaved identically and could be propagated in different cyprinid cell lines forming large syncytia. The virus was sensitive to lipid solvents and neither exhibited haemadsorption/haemagglutination nor reverse transcriptase activity. Mature virus particles displayed a spherical shape with diameter of 100-350 nm after negative staining and 100-300 nm in ultrathin sections, covered by short projections of 8-10 nm in length. Maturation of virus progeny was shown to occur by budding and envelopment of the filamentous helical nucleocapsids at the cell surface. A detailed comparison of ultrastructure and morphogenesis of the novel virus isolates with selected arena-, ortho- and paramyxoviruses as possible candidates for evaluation of taxonomic classification yielded no consistency in all phenotypic features. Thus, on the basis of ultrastructure the novel virus isolates could not be assigned unequivocally to any established virus family.
Collapse
Affiliation(s)
- H Granzow
- Institute of Infectology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Insel Riems, Germany
| | | | | | | | | | | | | |
Collapse
|
24
|
Kleines M, Häusler M, Krüttgen A, Scheithauer S. WU Polyomavirus (WUPyV): A Recently Detected Virus Causing Respiratory Disease? Viruses 2009; 1:678-88. [PMID: 21994565 PMCID: PMC3185540 DOI: 10.3390/v1030678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 10/19/2009] [Accepted: 11/04/2009] [Indexed: 11/16/2022] Open
Abstract
The WU polyomavirus (WUPyV) is a novel member of the family Polyomaviridae recently detected in respiratory tract specimens by shotgun sequencing. Intriguingly, viral genome has been detected in 0.4% to 11.5% of respiratory tract specimens from children with respiratory disease. The levels of co-infection with established respiratory viruses were in the range between 30.8% and 91.7%. Moreover, some studies report detection of WUPyV in stool or serum. So far, WUPyV infections can not be distinguished from other viral infections by means of clinical symptoms. Respiratory tract disease like pneumonia or bronchitis is frequently observed in patients harbouring WUPyV. Detection of viremia suggests systemic infections. However, the available data do not prove WUPyV to be a human pathogen. Further investigations are necessary.
Collapse
Affiliation(s)
- Michael Kleines
- Division of Virology, Department of Medical Microbiology, University Hospital Aachen, RWTH Aachen, Pauwelsstrasse 30, 52074 Aachen, Germany; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +49 241 808 8573; Fax: +49 241 808 2483
| | - Martin Häusler
- Deparment of Pediatrics, University Hospital Aachen, RWTH Aachen, Pauwelsstrasse 30, 52074 Aachen, Germany; E-Mail:
| | - Alexander Krüttgen
- Division of Virology, Department of Medical Microbiology, University Hospital Aachen, RWTH Aachen, Pauwelsstrasse 30, 52074 Aachen, Germany; E-Mail:
| | - Simone Scheithauer
- Department of Infection Control and Infectious Diseases, University Hospital Aachen, RWTH Aachen, Pauwelsstrasse 30, 52074 Aachen, Germany; E-Mail:
| |
Collapse
|