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Tomazin R, Cerar Kišek T, Janko T, Triglav T, Strašek Smrdel K, Cvitković Špik V, Kukec A, Mulec J, Matos T. Comparison of Culture-Dependent and Culture-Independent Methods for Routine Identification of Airborne Microorganisms in Speleotherapeutic Caves. Microorganisms 2024; 12:1427. [PMID: 39065195 PMCID: PMC11278542 DOI: 10.3390/microorganisms12071427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
The effective identification of bacterial and fungal isolates is essential for microbiological monitoring in environments like speleotherapeutic caves. This study compares MALDI-TOF MS and the OmniLog ID System, two high-throughput culture-based identification methods. MALDI-TOF MS identified 80.0% of bacterial isolates to the species level, while the OmniLog ID System identified 92.9%. However, species-level matches between the methods were only 48.8%, revealing considerable discrepancies. For discrepant results, MALDI-TOF MS matched molecular identification at the genus level in 90.5% of cases, while the OmniLog ID System matched only in 28.6%, demonstrating MALDI-TOF MS's superiority. The OmniLog ID System had difficulties identifying genera from the order Micrococcales. Fungal identification success with MALDI-TOF MS was 30.6% at the species level, potentially improvable with a customised spectral library, compared to the OmniLog ID System's 16.7%. Metagenomic approaches detected around 100 times more microbial taxa than culture-based methods, highlighting human-associated microorganisms, especially Staphylococcus spp. In addition to Staphylococcus spp. and Micrococcus spp. as indicators of cave anthropisation, metagenomics revealed another indicator, Cutibacterium acnes. This study advocates a multi-method approach combining MALDI-TOF MS, the OmniLog ID System, culture-based, and metagenomic analyses for comprehensive microbial identification. Metagenomic sampling on nitrocellulose filters provided superior read quality and microbial representation over liquid sampling, making it preferable for cave air sample collection.
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Affiliation(s)
- Rok Tomazin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia; (R.T.); (T.T.); (K.S.S.); (V.C.Š.)
| | - Tjaša Cerar Kišek
- National Laboratory for Health, Environment and Food, Department for Public Health Microbiology, Grablovičeva Ulica 44, SI-1000 Ljubljana, Slovenia; (T.C.K.); (T.J.)
| | - Tea Janko
- National Laboratory for Health, Environment and Food, Department for Public Health Microbiology, Grablovičeva Ulica 44, SI-1000 Ljubljana, Slovenia; (T.C.K.); (T.J.)
| | - Tina Triglav
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia; (R.T.); (T.T.); (K.S.S.); (V.C.Š.)
| | - Katja Strašek Smrdel
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia; (R.T.); (T.T.); (K.S.S.); (V.C.Š.)
| | - Vesna Cvitković Špik
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia; (R.T.); (T.T.); (K.S.S.); (V.C.Š.)
| | - Andreja Kukec
- Department of Public Health, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia;
| | - Janez Mulec
- Karst Research Institute, Research Centre of the Slovenian Academy of Sciences and Arts, Titov Trg 2, SI-6230 Postojna, Slovenia;
- UNESCO Chair on Karst Education, University of Nova Gorica, SI-5271 Vipava, Slovenia
| | - Tadeja Matos
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia; (R.T.); (T.T.); (K.S.S.); (V.C.Š.)
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2
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Goletic S, Goletic T, Omeragic J, Supic J, Kapo N, Nicevic M, Skapur V, Rukavina D, Maksimovic Z, Softic A, Alic A. Metagenomic Sequencing of Lloviu Virus from Dead Schreiber's Bats in Bosnia and Herzegovina. Microorganisms 2023; 11:2892. [PMID: 38138036 PMCID: PMC10745292 DOI: 10.3390/microorganisms11122892] [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: 10/08/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 12/24/2023] Open
Abstract
Bats are a natural host for a number of viruses, many of which are zoonotic and thus present a threat to human health. RNA viruses of the family Filoviridae, many of which cause disease in humans, have been associated with specific bat hosts. Lloviu virus is a Filovirus which has been connected to mass mortality events in Miniopterus schreibersii colonies in Spain and Hungary, and some studies have indicated its immense zoonotic potential. A die-off has been recorded among Miniopterus schreibersii in eastern Bosnia and Herzegovina for the first time, prompting the investigation to determine the causative agent. Bat carcasses were collected and subjected to pathological examination, after which the lung samples with notable histopathological changes, lung samples with no changes and guano were analyzed using metagenomic sequencing and RT-PCR. A partial Lloviu virus genome was sequenced from lung samples with histopathological changes and found to be closely related to Hungarian and Italian virus sequences. Further accumulation of mutations on the GP gene, coding the glycoprotein responsible for cell tropism and host preference, enhances the need for further characterization and monitoring of this virus to prevent spillover events and protect human health.
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Affiliation(s)
- Sejla Goletic
- University of Sarajevo—Veterinary Faculty, 71000 Sarajevo, Bosnia and Herzegovina; (S.G.); (J.O.); (J.S.); (N.K.); (M.N.); (D.R.); (Z.M.); (A.S.); (A.A.)
| | - Teufik Goletic
- University of Sarajevo—Veterinary Faculty, 71000 Sarajevo, Bosnia and Herzegovina; (S.G.); (J.O.); (J.S.); (N.K.); (M.N.); (D.R.); (Z.M.); (A.S.); (A.A.)
| | - Jasmin Omeragic
- University of Sarajevo—Veterinary Faculty, 71000 Sarajevo, Bosnia and Herzegovina; (S.G.); (J.O.); (J.S.); (N.K.); (M.N.); (D.R.); (Z.M.); (A.S.); (A.A.)
| | - Jovana Supic
- University of Sarajevo—Veterinary Faculty, 71000 Sarajevo, Bosnia and Herzegovina; (S.G.); (J.O.); (J.S.); (N.K.); (M.N.); (D.R.); (Z.M.); (A.S.); (A.A.)
| | - Naida Kapo
- University of Sarajevo—Veterinary Faculty, 71000 Sarajevo, Bosnia and Herzegovina; (S.G.); (J.O.); (J.S.); (N.K.); (M.N.); (D.R.); (Z.M.); (A.S.); (A.A.)
| | - Melisa Nicevic
- University of Sarajevo—Veterinary Faculty, 71000 Sarajevo, Bosnia and Herzegovina; (S.G.); (J.O.); (J.S.); (N.K.); (M.N.); (D.R.); (Z.M.); (A.S.); (A.A.)
| | - Vedad Skapur
- University of Sarajevo—Faculty of Agriculture and Food Sciences, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Dunja Rukavina
- University of Sarajevo—Veterinary Faculty, 71000 Sarajevo, Bosnia and Herzegovina; (S.G.); (J.O.); (J.S.); (N.K.); (M.N.); (D.R.); (Z.M.); (A.S.); (A.A.)
| | - Zinka Maksimovic
- University of Sarajevo—Veterinary Faculty, 71000 Sarajevo, Bosnia and Herzegovina; (S.G.); (J.O.); (J.S.); (N.K.); (M.N.); (D.R.); (Z.M.); (A.S.); (A.A.)
| | - Adis Softic
- University of Sarajevo—Veterinary Faculty, 71000 Sarajevo, Bosnia and Herzegovina; (S.G.); (J.O.); (J.S.); (N.K.); (M.N.); (D.R.); (Z.M.); (A.S.); (A.A.)
| | - Amer Alic
- University of Sarajevo—Veterinary Faculty, 71000 Sarajevo, Bosnia and Herzegovina; (S.G.); (J.O.); (J.S.); (N.K.); (M.N.); (D.R.); (Z.M.); (A.S.); (A.A.)
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3
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Vidovszky MZ, Kapitány S, Gellért Á, Harrach B, Görföl T, Boldogh SA, Kohl C, Wibbelt G, Mühldorfer K, Kemenesi G, Gembu GC, Hassanin A, Tu VT, Estók P, Horváth A, Kaján GL. Detection and genetic characterization of circoviruses in more than 80 bat species from eight countries on four continents. Vet Res Commun 2023; 47:1561-1573. [PMID: 37002455 PMCID: PMC10066014 DOI: 10.1007/s11259-023-10111-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/19/2023] [Indexed: 04/03/2023]
Abstract
Several bat-associated circoviruses and circular rep-encoding single-stranded DNA (CRESS DNA) viruses have been described, but the exact diversity and host species of these viruses are often unknown. Our goal was to describe the diversity of bat-associated circoviruses and cirliviruses, thus, 424 bat samples from more than 80 species were collected on four continents. The samples were screened for circoviruses using PCR and the resulting amino acid sequences were subjected to phylogenetic analysis. The majority of bat strains were classified in the genus Circovirus and some strains in the genus Cyclovirus and the clades CRESS1 and CRESS3. Some strains, however, could only be classified at the taxonomic level of the order and were not classified in any of the accepted or proposed clades. In the family Circoviridae, 71 new species have been predicted. This screening of bat samples revealed a great diversity of circoviruses and cirliviruses. These studies underline the importance of the discovery and description of new cirliviruses and the need to establish new species and families in the order Cirlivirales.
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Affiliation(s)
| | | | - Ákos Gellért
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Balázs Harrach
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Tamás Görföl
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
| | | | - Claudia Kohl
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Gudrun Wibbelt
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Kristin Mühldorfer
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Gábor Kemenesi
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
| | - Guy-Crispin Gembu
- Faculté des Sciences, Université de Kisangani, Kisangani, République Démocratique du Congo
| | - Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Péter Estók
- Department of Zoology, Eszterházy Károly Catholic University, Eger, Hungary
| | - Anna Horváth
- QUIRÓN, Center for Equine Assisted Interventions and Training for Well-Being and Sustainability, Comitán de Domínguez, Mexico
| | - Győző L. Kaján
- Veterinary Medical Research Institute, Budapest, Hungary
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Brnić D, Lojkić I, Krešić N, Zrnčić V, Ružanović L, Mikuletič T, Bosilj M, Steyer A, Keros T, Habrun B, Jemeršić L. Circulation of SARS-CoV-Related Coronaviruses and Alphacoronaviruses in Bats from Croatia. Microorganisms 2023; 11:microorganisms11040959. [PMID: 37110383 PMCID: PMC10143505 DOI: 10.3390/microorganisms11040959] [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: 02/24/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Bats are natural hosts of various coronaviruses (CoVs), including human CoVs, via an assumed direct zoonotic spillover or intermediate animal host. The present study aimed to investigate the circulation of CoVs in a bat colony in the Mediterranean region of Croatia. Guano and individual droppings from four bat species were sampled and tested with the E-gene sarbecovirus RT-qPCR, the pan-CoV semi-nested RT-PCR targeting the RdRp gene and NGS. Furthermore, bat blood samples were investigated for the presence of sarbecovirus-specific antibodies with the surrogate virus neutralization test (sVNT). The initial testing showed E-gene Sarebeco RT-qPCR reactivity in 26% of guano samples while the bat droppings tested negative. The application of RdRp semi-nested RT-PCR and NGS revealed the circulation of bat alpha- and betaCoVs. Phylogenetic analysis confirmed the clustering of betaCoV sequence with SARS-CoV-related bat sarbecoviruses and alpha-CoV sequences with representatives of the Minunacovirus subgenus. The results of sVNT show that 29% of bat sera originated from all four species that tested positive. Our results are the first evidence of the circulation of SARS-CoV-related coronaviruses in bats from Croatia.
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Affiliation(s)
- Dragan Brnić
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Ivana Lojkić
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Nina Krešić
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Vida Zrnčić
- Croatian Biospeleological Society, Demetrova 1, 10000 Zagreb, Croatia
| | - Lea Ružanović
- Croatian Biospeleological Society, Demetrova 1, 10000 Zagreb, Croatia
| | - Tina Mikuletič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Martin Bosilj
- National Laboratory of Health, Environment and Food, Grablovičeva 44, 1000 Ljubljana, Slovenia
| | - Andrej Steyer
- National Laboratory of Health, Environment and Food, Grablovičeva 44, 1000 Ljubljana, Slovenia
| | - Tomislav Keros
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Boris Habrun
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Lorena Jemeršić
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
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Ramos EDSF, Abreu WU, Rodrigues LRR, Marinho LF, Morais VDS, Villanova F, Pandey RP, Araújo ELL, Deng X, Delwart E, da Costa AC, Leal E. Novel Chaphamaparvovirus in Insectivorous Molossus molossus Bats, from the Brazilian Amazon Region. Viruses 2023; 15:606. [PMID: 36992315 PMCID: PMC10054343 DOI: 10.3390/v15030606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 02/25/2023] Open
Abstract
Chaphamaparvovirus (CHPV) is a recently characterized genus of the Parvoviridae family whose members can infect different hosts, including bats, which constitute the second most diverse order of mammals and are described worldwide as important transmitters of zoonotic diseases. In this study, we identified a new CHPV in bat samples from the municipality of Santarém (Pará state, North Brazil). A total of 18 Molossus molossus bats were analyzed using viral metagenomics. In five animals, we identified CHPVs. These CHPV sequences presented the genome with a size ranging from 3797 to 4284 bp. Phylogenetic analysis-based nucleotide and amino acid sequences of the VP1 and NS1 regions showed that all CHPV sequences are monophyletic. They are also closely related to CHPV sequences previously identified in bats in southern and southeast Brazil. According to the International Committee on Taxonomy of Viruses (ICTV) classification criteria for this species (the CHPV NS1 gene region must have 85% identity to be classified in the same species), our sequences are likely a new specie within the genus Chaphamaparvovirus, since they have less than 80% identity with other CHPV described earlier in bats. We also make some phylogenetic considerations about the interaction between CHPV and their host. We suggest a high level of specificity of CPHV and its hosts. Thus, the findings contribute to improving information about the viral diversity of parvoviruses and show the importance of better investigating bats, considering that they harbor a variety of viruses that may favor zoonotic events.
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Affiliation(s)
- Endrya do Socorro Foro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
| | - Wandercleyson Uchôa Abreu
- Programa de Pos-Graduação REDE Bionorte, Polo Pará, Universidade Federal do Oeste do Pará, Santarém 68040-255, Pará, Brazil
| | - Luis Reginaldo Ribeiro Rodrigues
- Laboratory of Genetics & Biodiversity, Institute of Educational Sciences, Universidade Federal do Oeste do Pará, Santarém 68040-255, Pará, Brazil
| | - Luis Fernando Marinho
- Department of Agricultural Sciences, School of Veterinary Medicine, University of Amazonia, Santarém 68040-255, Pará, Brazil
| | - Vanessa dos Santos Morais
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, São Paulo, Brazil
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health, Surveillance Secretariat, Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Distrito Federal, Brazil
| | - Xutao Deng
- General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health, Surveillance Secretariat, Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Distrito Federal, Brazil
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
- Vitalant Research Institute, San Francisco, CA 94143, USA
| | - Antonio Charlys da Costa
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, São Paulo, Brazil
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
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6
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Cholleti H, de Jong J, Blomström AL, Berg M. Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats. Pathogens 2022; 12:pathogens12010012. [PMID: 36678360 PMCID: PMC9861107 DOI: 10.3390/pathogens12010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Bats are reservoirs for many different viruses, including some that can be transmitted to and cause disease in humans and/or animals. However, less is known about the bat-borne viruses circulating in Northern European countries such as in Sweden. In this study, saliva from Myotis brandtii bats, collected from south-central Sweden, was analyzed for viruses. The metagenomic analysis identified viral sequences belonging to different viral families, including, e.g., Nairoviridae, Retroviridae, Poxviridae, Herpesviridae and Siphoviridae. Interestingly, through the data analysis, the near-complete genome of Issyk-Kul virus (ISKV), a zoonotic virus within the Nairoviridae family, was obtained, showing 95-99% protein sequence identity to previously described ISKVs. This virus is believed to infect humans via an intermediate tick host or through contact with bat excrete. ISKV has previously been found in bats in Europe, but not previously in the Nordic region. In addition, near full-length genomes of two novel viruses belonging to Picornavirales order and Tymoviridae family were characterized. Taken together, our study has not only identified novel viruses, but also the presence of a zoonotic virus not previously known to circulate in this region. Thus, the results from these types of studies can help us to better understand the diversity of viruses circulating in bat populations, as well as identify viruses with zoonotic potential that could possibly be transmitted to humans.
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Affiliation(s)
- Harindranath Cholleti
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden
- Correspondence:
| | - Johnny de Jong
- Swedish Biodiversity Centre (CBM), SLU, P.O. Box 7016, 750 07 Uppsala, Sweden
| | - Anne-Lie Blomström
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden
| | - Mikael Berg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden
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7
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Elimination of Foreign Sequences in Eukaryotic Viral Reference Genomes Improves the Accuracy of Virome Analysis. mSystems 2022; 7:e0090722. [PMID: 36286492 PMCID: PMC9765019 DOI: 10.1128/msystems.00907-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Widespread in public databases, foreign contaminant sequences pose a substantial obstacle in genomic analyses. Such contamination in viral genome databases is also notorious but more complicated and often causes questionable results in various applications, particularly in virome-based virus detection. Here, we conducted comprehensive screening and identification of the foreign sequences hidden in the largest eukaryotic viral genome collections of GenBank and UniProt using a scrutiny pipeline, which enables us to rigorously detect those problematic viral sequences (PVSs) with origins in hosts, vectors, and laboratory components. As a result, a total of 766 nucleotide PVSs and 276 amino acid PVSs with lengths up to 6,605 bp were determined, which were widely distributed in 39 families with many involving highly public health-concerning viruses, such as hepatitis C virus, Crimean-Congo hemorrhagic fever virus, and filovirus. The majority of these PVSs are genomic fragments of hosts including humans and bacteria. However, they cannot simply be regarded as foreign contaminants, since parts of them are results of natural occurrence or artificial engineering of viruses. Nevertheless, they severely disturb such sequence-based analyses as genome annotation, taxonomic assignment, and virome profiling. Therefore, we provide a clean version of the eukaryotic viral reference data set by the removal of these PVSs, which allows more accurate virome analysis with less time consumed than with other comprehensive databases. IMPORTANCE High-throughput sequencing-based viromics highly depends on reference databases, but foreign contamination is widespread in public databases and often leads to confusing and even wrong conclusions in genomic analysis and viromic profiling. To address this issue, we systematically detected and identified the contamination in the largest viral sequence collections of GenBank and UniProt based on a stringent scrutiny pipeline. We found hundreds of PVSs that are related to hosts, vectors, and laboratory components. By the removal of them, the resulting data set greatly improves the accuracy and efficiency of eukaryotic virome profiling. These results refresh our knowledge of the type and origin of PVSs and also have warning implications for viromic analysis. Viromic practitioners should be aware of these problems caused by PVSs and need to realize that a careful review of bioinformatic results is necessary for a reliable conclusion.
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Kamani J, González-Miguel J, Msheliza EG, Goldberg TL. Straw-Colored Fruit Bats ( Eidolon helvum) and Their Bat Flies ( Cyclopodia greefi) in Nigeria Host Viruses with Multifarious Modes of Transmission. Vector Borne Zoonotic Dis 2022; 22:545-552. [DOI: 10.1089/vbz.2022.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Joshua Kamani
- Parasitology Division, National Veterinary Research Institute (NVRI), Vom, Nigeria
| | - Javier González-Miguel
- Laboratory of Parasitology, Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Salamanca, Spain
- Molecular Parasitology Laboratory, Centre of One Health (COH), Ryan Institute, National University of Ireland, Galway, Ireland
| | - Emmanuel G. Msheliza
- Parasitology Division, National Veterinary Research Institute (NVRI), Vom, Nigeria
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
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9
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Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland. Viruses 2022; 14:v14091911. [PMID: 36146717 PMCID: PMC9505930 DOI: 10.3390/v14091911] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/08/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Bats are increasingly recognized as reservoirs for many different viruses that threaten public health, such as Hendravirus, Ebolavirus, Nipahvirus, and SARS- and MERS-coronavirus. To assess spillover risk, viromes of bats from different parts of the world have been investigated in the past. As opposed to most of these prior studies, which determined the bat virome at a single time point, the current work was performed to monitor changes over time. Specifically, fecal samples of three endemic Swiss bat colonies consisting of three different bat species were collected over three years and analyzed using next-generation sequencing. Furthermore, single nucleotide variants of selected DNA and RNA viruses were analyzed to investigate virus genome evolution. In total, sequences of 22 different virus families were found, of which 13 are known to infect vertebrates. Most interestingly, in a Vespertilio murinus colony, sequences from a MERS-related beta-coronavirus were consistently detected over three consecutive years, which allowed us to investigate viral genome evolution in a natural reservoir host.
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Cholleti H, de Jong J, Blomström AL, Berg M. Characterization of Pipistrellus pygmaeus Bat Virome from Sweden. Viruses 2022; 14:v14081654. [PMID: 36016275 PMCID: PMC9415950 DOI: 10.3390/v14081654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/27/2022] [Accepted: 07/24/2022] [Indexed: 11/25/2022] Open
Abstract
Increasing amounts of data indicate that bats harbor a higher viral diversity relative to other mammalian orders, and they have been recognized as potential reservoirs for pathogenic viruses, such as the Hendra, Nipah, Marburg, and SARS-CoV viruses. Here, we present the first viral metagenomic analysis of Pipistrellus pygmaeus from Uppsala, Sweden. Total RNA was extracted from the saliva and feces of individual bats and analyzed using Illumina sequencing. The results identified sequences related to 51 different viral families, including vertebrate, invertebrate, and plant viruses. These viral families include Coronaviridae, Picornaviridae, Dicistroviridae, Astroviridae, Hepeviridae, Reoviridae, Botourmiaviridae, Lispviridae, Totiviridae, Botoumiaviridae, Parvoviridae, Retroviridae, Adenoviridae, and Partitiviridae, as well as different unclassified viruses. We further characterized three near full-length genome sequences of bat coronaviruses. A phylogenetic analysis showed that these belonged to alphacoronaviruses with the closest similarity (78–99% at the protein level) to Danish and Finnish bat coronaviruses detected in Pipistrellus and Myotis bats. In addition, the full-length and the near full-length genomes of picornavirus were characterized. These showed the closest similarity (88–94% at the protein level) to bat picornaviruses identified in Chinese bats. Altogether, the results of this study show that Swedish Pipistrellus bats harbor a great diversity of viruses, some of which are closely related to mammalian viruses. This study expands our knowledge on the bat population virome and improves our understanding of the evolution and transmission of viruses among bats and to other species.
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Affiliation(s)
- Harindranath Cholleti
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden; (A.-L.B.); (M.B.)
- Correspondence:
| | - Johnny de Jong
- Swedish Biodiversity Centre (CBM), Department of Urban and Rural Development, Swedish University of Agricultural Sciences (SLU), P.O. Box 7016, 750 07 Uppsala, Sweden;
| | - Anne-Lie Blomström
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden; (A.-L.B.); (M.B.)
| | - Mikael Berg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden; (A.-L.B.); (M.B.)
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11
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Sanyal A, Agarwal S, Ramakrishnan U, Garg KM, Chattopadhyay B. Using Environmental Sampling to Enable Zoonotic Pandemic Preparedness. J Indian Inst Sci 2022; 102:711-730. [PMID: 36093274 PMCID: PMC9449264 DOI: 10.1007/s41745-022-00322-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/27/2022] [Indexed: 11/28/2022]
Abstract
The current pandemic caused by the SARS CoV-2, tracing back its origin possibly to a coronavirus associated with bats, has ignited renewed interest in understanding zoonotic spillovers across the globe. While research is more directed towards solving the problem at hand by finding therapeutic strategies and novel vaccine techniques, it is important to address the environmental drivers of pathogen spillover and the complex biotic and abiotic drivers of zoonoses. The availability of cutting-edge genomic technologies has contributed enormously to preempt viral emergence from wildlife. However, there is still a dearth of studies from species-rich South Asian countries, especially from India. In this review, we outline the importance of studying disease dynamics through environmental sampling from wildlife in India and how ecological parameters of both the virus and the host community may play a role in mediating cross-species spillovers. Non-invasive sampling using feces, urine, shed hair, saliva, shed skin, and feathers has been instrumental in providing genetic information for both the host and their associated pathogens. Here, we discuss the advances made in environmental sampling protocols and strategies to generate genetic data from such samples towards the surveillance and characterization of potentially zoonotic pathogens. We primarily focus on bat-borne or small mammal-borne zoonoses and propose a conceptual framework for non-invasive strategies to tackle the threat of emerging zoonotic infections.
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12
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Bolatti EM, Viarengo G, Zorec TM, Cerri A, Montani ME, Hosnjak L, Casal PE, Bortolotto E, Di Domenica V, Chouhy D, Allasia MB, Barquez RM, Poljak M, Giri AA. Viral Metagenomic Data Analyses of Five New World Bat Species from Argentina: Identification of 35 Novel DNA Viruses. Microorganisms 2022; 10:microorganisms10020266. [PMID: 35208721 PMCID: PMC8880087 DOI: 10.3390/microorganisms10020266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/18/2022] Open
Abstract
Bats are natural reservoirs of a variety of zoonotic viruses, many of which cause severe human diseases. Characterizing viruses of bats inhabiting different geographical regions is important for understanding their viral diversity and for detecting viral spillovers between animal species. Herein, the diversity of DNA viruses of five arthropodophagous bat species from Argentina was investigated using metagenomics. Fecal samples of 29 individuals from five species (Tadarida brasiliensis, Molossus molossus, Eumops bonariensis, Eumops patagonicus, and Eptesicus diminutus) living at two different geographical locations, were investigated. Enriched viral DNA was sequenced using Illumina MiSeq, and the reads were trimmed and filtered using several bioinformatic approaches. The resulting nucleotide sequences were subjected to viral taxonomic classification. In total, 4,520,370 read pairs were sequestered by sequencing, and 21.1% of them mapped to viral taxa. Circoviridae and Genomoviridae were the most prevalent among vertebrate viral families in all bat species included in this study. Samples from the T. brasiliensis colony exhibited lower viral diversity than samples from other species of New World bats. We characterized 35 complete genome sequences of novel viruses. These findings provide new insights into the global diversity of bat viruses in poorly studied species, contributing to prevention of emerging zoonotic diseases and to conservation policies for endangered species.
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Affiliation(s)
- Elisa M. Bolatti
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Gastón Viarengo
- DETx MOL S.A., Centro Científico Tecnológico CONICET Rosario, Ocampo y Esmeralda, Rosario 2000, Argentina;
| | - Tomaz M. Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
| | - Agustina Cerri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
| | - María E. Montani
- Museo Provincial de Ciencias Naturales “Dr. Ángel Gallardo”, San Lorenzo 1949, Rosario 2000, Argentina;
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina; (V.D.D.); (R.M.B.)
- Instituto PIDBA (Programa de Investigaciones de Biodiversidad Argentina), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán 4000, Argentina
| | - Lea Hosnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
| | - Pablo E. Casal
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Eugenia Bortolotto
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina; (E.B.); (M.B.A.)
| | - Violeta Di Domenica
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina; (V.D.D.); (R.M.B.)
| | - Diego Chouhy
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
- DETx MOL S.A., Centro Científico Tecnológico CONICET Rosario, Ocampo y Esmeralda, Rosario 2000, Argentina;
| | - María Belén Allasia
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina; (E.B.); (M.B.A.)
| | - Rubén M. Barquez
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina; (V.D.D.); (R.M.B.)
- Instituto PIDBA (Programa de Investigaciones de Biodiversidad Argentina), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán 4000, Argentina
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
- Correspondence: (M.P.); (A.A.G.); Tel.: +386-1-543-7454 (M.P.); +54-341-435-0661 (ext. 116) (A.A.G.); Fax: +54-341-439-0465 (A.A.G.)
| | - Adriana A. Giri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
- Correspondence: (M.P.); (A.A.G.); Tel.: +386-1-543-7454 (M.P.); +54-341-435-0661 (ext. 116) (A.A.G.); Fax: +54-341-439-0465 (A.A.G.)
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13
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Zoonotic disease and virome diversity in bats. Curr Opin Virol 2021; 52:192-202. [PMID: 34954661 PMCID: PMC8696223 DOI: 10.1016/j.coviro.2021.12.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/19/2021] [Accepted: 12/06/2021] [Indexed: 02/08/2023]
Abstract
The emergence of zoonotic viral diseases in humans commonly reflects exposure to mammalian wildlife. Bats (order Chiroptera) are arguably the most important mammalian reservoir for zoonotic viruses, with notable examples including Severe Acute Respiratory Syndrome coronaviruses 1 and 2, Middle East Respiratory Syndrome coronavirus, henipaviruses and lyssaviruses. Herein, we outline our current knowledge on the diversity of bat viromes, particularly through the lens of metagenomic next-generation sequencing and in the context of disease emergence. A key conclusion is that although bats harbour abundant virus diversity, the vast majority of bat viruses have not emerged to cause disease in new hosts such that bats are better regarded as critical but endangered components of global ecosystems.
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14
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Abstract
Bats are infamous reservoirs of deadly human viruses. While retroviruses, such as the human immunodeficiency virus (HIV), are among the most significant of virus families that have jumped from animals into humans, whether bat retroviruses have the potential to infect and cause disease in humans remains unknown. Recent reports of retroviruses circulating in bat populations builds on two decades of research describing the fossil records of retroviral sequences in bat genomes and of viral metagenomes extracted from bat samples. The impact of the global COVID-19 pandemic demands that we pay closer attention to viruses hosted by bats and their potential as a zoonotic threat. Here we review current knowledge of bat retroviruses and explore the question of whether they represent a threat to humans.
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Affiliation(s)
- Joshua A. Hayward
- Health Security Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Gilda Tachedjian
- Health Security Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
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15
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Update on Potentially Zoonotic Viruses of European Bats. Vaccines (Basel) 2021; 9:vaccines9070690. [PMID: 34201666 PMCID: PMC8310327 DOI: 10.3390/vaccines9070690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/10/2021] [Accepted: 06/21/2021] [Indexed: 12/13/2022] Open
Abstract
Bats have been increasingly gaining attention as potential reservoir hosts of some of the most virulent viruses known. Numerous review articles summarize bats as potential reservoir hosts of human-pathogenic zoonotic viruses. For European bats, just one review article is available that we published in 2014. The present review provides an update on the earlier article and summarizes the most important viruses found in European bats and their possible implications for Public Health. We identify the research gaps and recommend monitoring of these viruses.
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16
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Hardmeier I, Aeberhard N, Qi W, Schoenbaechler K, Kraettli H, Hatt JM, Fraefel C, Kubacki J. Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses. PLoS One 2021; 16:e0252534. [PMID: 34133435 PMCID: PMC8208571 DOI: 10.1371/journal.pone.0252534] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/17/2021] [Indexed: 01/02/2023] Open
Abstract
Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.
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Affiliation(s)
| | - Nadja Aeberhard
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, Zurich, Switzerland
| | | | | | - Jean-Michel Hatt
- Clinic for Zoo Animals, Exotic Pets and Wildlife, University of Zurich, Zurich, Switzerland
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Jakub Kubacki
- Institute of Virology, University of Zurich, Zurich, Switzerland
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17
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Jia W, Wang F, Li J, Chang X, Yang Y, Yao H, Bao Y, Song Q, Ye G. A Novel Iflavirus Was Discovered in Green Rice Leafhopper Nephotettix cincticeps and Its Proliferation Was Inhibited by Infection of Rice Dwarf Virus. Front Microbiol 2021; 11:621141. [PMID: 33488564 PMCID: PMC7820178 DOI: 10.3389/fmicb.2020.621141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022] Open
Abstract
The green rice leafhopper, Nephotettix cincticeps (Hemiptera: Cicadellidae), is a key insect vector transmitting rice dwarf virus (RDV) that causes rice dwarf disease. We discovered a novel iflavirus from the transcriptomes of N. cincticeps and named it as Nephotettix cincticeps positive-stranded RNA virus-1 (NcPSRV-1). The viral genome consists of 10,524 nucleotides excluding the poly(A) tail and contains one predicted open reading frame encoding a polyprotein of 3,192 amino acids, flanked by 5' and 3' untranslated regions. NcPSRV-1 has a typical iflavirus genome arrangement and is clustered with the members of the family Iflaviridae in the phylogenetic analysis. NcPSRV-1 was detected in all tested tissues and life stages of N. cincticeps and could be transmitted horizontally and vertically. Moreover, NcPSRV-1 had high prevalence in the laboratory populations and was widely spread in field populations of N. cincticeps. NcPSRV-1 could also infect the two-striped leafhopper, Nephotettix apicalis, at a 3.33% infection rate, but was absent in the zigzag leafhopper, Recilia dorsalis, and rice Oryza sativa variety TN1. The infection of RDV altered the viral load and infection rate of NcPSRV-1 in N. cincticeps, for which it seems that RDV has an antagonistic effect on NcPSRV-1 infection in the host.
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Affiliation(s)
- Wenxi Jia
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jingjing Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, United States
| | - Xuefei Chang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yi Yang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hongwei Yao
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yanyuan Bao
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, United States
| | - Gongyin Ye
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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