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Larrea-Sarmiento A, Olmedo-Velarde A, Wang X, Borth W, Matsumoto TK, Suzuki JY, Wall MM, Melzer M, Hu J. A novel ampelovirus associated with mealybug wilt of pineapple (Ananas comosus). Virus Genes 2021; 57:464-468. [PMID: 34184183 DOI: 10.1007/s11262-021-01852-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/04/2021] [Indexed: 11/28/2022]
Abstract
Mealybug wilt of pineapple (MWP) is the most important and complex viral disease affecting pineapple worldwide. High-throughput sequencing was conducted to characterize a new virus identified only in symptomatic pineapple plants and tentatively named pineapple mealybug wilt-associated virus 6 (PMWaV-6). Data analyses revealed a genome of 17,854 nucleotides with an organization resembling members of the genus Ampelovirus, family Closteroviridae. Encoded proteins shared sequence identity with the corresponding proteins of grapevine leafroll-associated virus 3, blackberry vein banding-associated virus, and PMWaV-2. The present study reports the discovery of PMWaV-6, a putative and distinct new member of the genus Ampelovirus, subgroup I, its potential involvement in MWP, and the development of PMWaV-6-specific RT-PCR assays to detect and monitor this virus in field samples.
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Affiliation(s)
- Adriana Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, USA
| | - Alejandro Olmedo-Velarde
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, USA
| | - Xupeng Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, USA
| | - Wayne Borth
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, USA
| | - Tracie K Matsumoto
- United States Department of Agriculture, Agricultural Research Service, Daniel K. Inouye U. S. Pacific Basin Agricultural Research Center, Hilo, HI, USA
| | - Jon Y Suzuki
- United States Department of Agriculture, Agricultural Research Service, Daniel K. Inouye U. S. Pacific Basin Agricultural Research Center, Hilo, HI, USA
| | - Marisa M Wall
- United States Department of Agriculture, Agricultural Research Service, Daniel K. Inouye U. S. Pacific Basin Agricultural Research Center, Hilo, HI, USA
| | - Michael Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, USA
| | - John Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, USA.
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Petrzik K, Kmoch M, Brázdová S, Ševčík R. Complete genome sequences of novel Berlinvirus and novel Certrevirus lytic for Pectobacterium sp. causing soft rot and black leg disease of potato. Virus Genes 2021; 57:302-305. [PMID: 33914264 DOI: 10.1007/s11262-021-01838-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/19/2021] [Accepted: 04/23/2021] [Indexed: 11/25/2022]
Abstract
Two novel dsDNA bacteriophages named Pectobacterium virus CB251 (PcCB251) and Pectobacterium virus CB7V (PcCB7V) targeting plant pathogen Pectobacterium parmentieri have been isolated and sequenced. The PcCB251 genome consists of 40,557 bp with G+C content of 48.6% and contains 47 predicted genes on a single strand. The phage is classified in genus Berlinvirus, family Autographiviridae. The PcCB7V phage has a circular dsDNA genome of 146,054 bp with G+C content of 50.4% and contains 269 predicted protein genes on both strands and 13 tRNA genes. The PcCB7V phage can be classified in genus Certrevirus, subfamily Vequintavirinae. Both novel bacteriophages have narrow host ranges, but they extend the list of candidates for phage-based control of pectolytic bacteria causing soft rot disease of potato.
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Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic.
| | - Martin Kmoch
- Potato Research Institute Havlíčkův Brod, Dobrovského 2366, Havlíčkův Brod, 580 01, Czech Republic
| | - Sára Brázdová
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic
| | - Rudolf Ševčík
- University of Chemistry and Technology Prague, Technická 1905/5, Prague 6-Dejvice, Prague, Czech Republic
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Commodari E, La Rosa VL, Coniglio MA. Health risk perceptions in the era of the new coronavirus: are the Italian people ready for a novel virus? A cross-sectional study on perceived personal and comparative susceptibility for infectious diseases. Public Health 2020; 187:8-14. [PMID: 32866818 PMCID: PMC7396885 DOI: 10.1016/j.puhe.2020.07.036] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [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: 03/23/2020] [Revised: 07/05/2020] [Accepted: 07/26/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVES This study aims to evaluate the impact of psychological and sociodemographic variables on perceived personal and comparative susceptibility to diseases caused by a novel, unknown virus. STUDY DESIGN Cross-sectional study. METHODS A total of 438 adults (200 male and 238 female) were interviewed in the waiting rooms of three primary care medicine outpatient clinics. The participants completed three validated questionnaires: the Italian Adjustment of Risk Perception of Infectious Diseases questionnaire, the General Self-Efficacy (GSE) scale, and the Italian Version of Personality Inventory (ITAPI). RESULTS Only 5% of the respondents believed it likely that they would contract a disease caused by a novel virus in the following months, even though 5.9% considered this probability higher than that of other people of the same age and gender. Gender (P < .04), age (P = .002), and marital status (P = .002) significantly affected the perceived risk of getting a disease caused by a novel virus. Self-efficacy (P < .001), imagination (P < .001), and empathy (P < .001) were significant predictors of perceived personal susceptibility. Self-efficacy (P = .04) and imagination (P = .04) were predictive of perceived comparative susceptibility. CONCLUSIONS Adequate psycho-educational interventions are necessary to empower the population in adopting the necessary prevention and containment measures aimed at limiting the spread of novel diseases such as COVID-19 and avoiding disastrous consequences both at the health and economic level.
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Affiliation(s)
- E Commodari
- Department of Educational Sciences, University of Catania, Catania, Italy
| | - V L La Rosa
- Department of Educational Sciences, University of Catania, Catania, Italy.
| | - M A Coniglio
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, Catania, Italy
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Abstract
Cases of 2019-nCoV are now being reported in different regions around the globe, concerning for a possible SARS like epidemic that infected for than 8000 people in 2002-03. Though, major health authorities are still working on understanding the virus and its transmission, here we present a brief report regarding the 2019-nCoV outbreak and what is known so far.
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Naveen KP, Bhat AI. Development of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) assays for the detection of two novel viruses infecting ginger. J Virol Methods 2020; 282:113884. [PMID: 32442456 DOI: 10.1016/j.jviromet.2020.113884] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 12/25/2022]
Abstract
Our recent studies have shown the association of two novel viruses namely, ginger chlorotic fleck-associated virus 1 (GCFaV-1) and ginger chlorotic fleck-associated virus 2 (GCFaV-2) with chlorotic fleck disease of ginger. As ginger is propagated through vegetative means, the development of diagnostics would aid in the identification of virus-free plants. In the present study, reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) assays were developed and validated for the quick detection of GCFaV-1 and GCFaV-2. The detection limits of viruses by these assays, when compared with conventional and real-time RT-PCR, showed that RT-LAMP was up to 1000 times more sensitive than conventional RT-PCR and one-hundredth that of real-time RT-PCR for both the viruses. The detection limit of RT-RPA for GCFaV-1 was up to 100 times more than that of RT-PCR and one-thousandth that of real-time RT-PCR. On the other hand, for detecting GCFaV-2, RT-RPA was found up to 1000 times more sensitive than conventional RT-PCR and one hundredth that of real-time RT-PCR. Based on the cost-effectiveness and duration, RT-LAMP and RT-RPA assays can be suggested for the rapid detection of both viruses.
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Affiliation(s)
- K P Naveen
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu, Kozhikode 673012, India
| | - A I Bhat
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu, Kozhikode 673012, India.
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Guan TP, Teng JLL, Yeong KY, You ZQ, Liu H, Wong SSY, Lau SKP, Woo PCY. Metagenomic analysis of Sichuan takin fecal sample viromes reveals novel enterovirus and astrovirus. Virology 2018; 521:77-91. [PMID: 29886344 DOI: 10.1016/j.virol.2018.05.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 05/30/2018] [Indexed: 12/27/2022]
Abstract
The Sichuan takin inhabits the bamboo forests in the Eastern Himalayas and is considered as a national treasure of China with the highest legal protection and conservation status considered as vulnerable according to The IUCN Red List of Threatened Species. In this study, fecal samples of 71 Sichuan takins were pooled and deep sequenced. Among the 103,553 viral sequences, 21,961 were assigned to mammalian viruses. De novo assembly revealed genomes of an enterovirus and an astrovirus and contigs of circoviruses and genogroup I picobirnaviruses. Complete genome sequencing and phylogenetic analysis showed that Sichuan takin enterovirus is a novel serotype/genotype of the species Enterovirus G, with evidence of recombination. Sichuan takin astrovirus is a new subtype of bovine astrovirus, probably belonging to a new genogroup in the genus Mamastrovirus. Further studies will reveal whether these viruses can also be found in Mishmi takin and Shaanxi takin and their pathogenic potentials.
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Zhao G, Wu G, Lim ES, Droit L, Krishnamurthy S, Barouch DH, Virgin HW, Wang D. VirusSeeker, a computational pipeline for virus discovery and virome composition analysis. Virology 2017; 503:21-30. [PMID: 28110145 DOI: 10.1016/j.virol.2017.01.005] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/07/2017] [Accepted: 01/10/2017] [Indexed: 01/21/2023]
Abstract
The advent of Next Generation Sequencing (NGS) has vastly increased our ability to discover novel viruses and to systematically define the spectrum of viruses present in a given specimen. Such studies have led to the discovery of novel viral pathogens as well as broader associations of the virome with diverse diseases including inflammatory bowel disease, severe acute malnutrition and HIV/AIDS. Critical to the success of these efforts are robust bioinformatic pipelines for rapid classification of microbial sequences. Existing computational tools are typically focused on either eukaryotic virus discovery or virome composition analysis but not both. Here we present VirusSeeker, a BLAST-based NGS data analysis pipeline designed for both purposes. VirusSeeker has been successfully applied in several previously published virome studies. Here we demonstrate the functionality of VirusSeeker in both novel virus discovery and virome composition analysis.
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Remoli ME, Jiménez M, Fortuna C, Benedetti E, Marchi A, Genovese D, Gramiccia M, Molina R, Ciufolini MG. Phleboviruses detection in Phlebotomus perniciosus from a human leishmaniasis focus in South-West Madrid region, Spain. Parasit Vectors 2016; 9:205. [PMID: 27075742 PMCID: PMC4831143 DOI: 10.1186/s13071-016-1488-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 11/26/2015] [Accepted: 04/03/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phlebotomus-borne (PhB-) viruses are distributed in large areas of the Old World and are widespread throughout the Mediterranean basin, where recent investigations have indicated that virus diversity is higher than initially suspected. Some of these viruses are causes of meningitis, encephalitis and febrile illnesses. In order to monitor the viral presence and the infection rate of PhB-viruses in a recently identified and well characterized human zoonotic leishmaniasis focus in southwestern Madrid, Spain, a sand fly collection was carried out. METHODS Sand fly insects were collected in four stations using CDC light traps during 2012-2013 summer seasons. Screening for Phlebovirus presence both via isolation on Vero cells and via polymerase chain reaction (PCR), using degenerated primers targeting a portion of the L segment, was performed. The serological identity and phylogenetic relationships on the three genomic segments of the viral isolates were carried out. RESULTS Six viral isolates belonging to different serological complexes of the genus Phlebovirus were obtained from fifty pools on a total of 963 P. perniciosus (202 females). Phylogenetic analysis and serological assays allowed the identification of two isolates of Toscana virus (TOSV) B genotype, three isolates strongly related to Italian Arbia virus (ARBV), and one isolate of a novel putative Phlebovirus related to the recently characterized Arrabida virus in South Portugal, tentatively named Arrabida-like virus. Positive male sand fly pools suggested that transovarial or venereal transmission could occur under natural conditions. CONCLUSIONS Our findings highlighted the presence of different Phlebovirus species in the South-West area of the Madrid Autonomous Community where an outbreak of cutaneous and visceral human leishmaniasis has been recently described. The evidence of viral species never identified before in Spain, as ARBV and Arrabida-like virus, and TOSV B genotype focus stability was demonstrated. Environmental aspects such as climate change, growing urbanization, socio-economic development could have contributed to the genesis of this wide ecological niche of PhB-viruses and Leishmania spp. The potential role of vertebrates as reservoir for the phleboviruses identified and the possibility of Phleboviruses-Leishmania co-infection in the same sand fly should be assessed. Furthermore the PhB-viruses impact on human health should be implemented.
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Affiliation(s)
- Maria Elena Remoli
- National Reference Laboratory for Arboviruses, Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Maribel Jiménez
- Unidad de EntomologíaMédica, Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo s/n, 28220, Majadahonda, Madrid, Spain
| | - Claudia Fortuna
- National Reference Laboratory for Arboviruses, Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Eleonora Benedetti
- National Reference Laboratory for Arboviruses, Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Antonella Marchi
- National Reference Laboratory for Arboviruses, Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Domenico Genovese
- Unit of Global Health, Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Marina Gramiccia
- Unit of Vector-borne Diseases and International Health, Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Ricardo Molina
- Unidad de EntomologíaMédica, Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo s/n, 28220, Majadahonda, Madrid, Spain
| | - Maria Grazia Ciufolini
- National Reference Laboratory for Arboviruses, Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
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Sakai K, Hagiwara K, Omatsu T, Hamasaki C, Kuwata R, Shimoda H, Suzuki K, Endoh D, Nagata N, Nagai M, Katayama Y, Oba M, Kurane I, Saijo M, Morikawa S, Mizutani T, Maeda K. Isolation and characterization of a novel Rhabdovirus from a wild boar (Sus scrofa) in Japan. Vet Microbiol 2015; 179:197-203. [PMID: 26116524 DOI: 10.1016/j.vetmic.2015.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 01/23/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 01/29/2023]
Abstract
A novel rhabdovirus was isolated from the serum of a healthy Japanese wild boar (Sus scrofa leucomystax) and identified using the rapid determination system for viral nucleic acid sequences (RDV), next-generation sequencing, and electron microscopy. The virus was tentatively named wild boar rhabdovirus 1 (WBRV1). Phylogenetic analysis of the entire genome sequence indicated that WBRV1 is closely related to Tupaia rhabdovirus (TRV), which was isolated from cultured cells of hepatocellular carcinoma tissue of tree shrew. TRV has not been assigned to any genus of Rhabdoviridae till date. Analysis of the L gene indicated that WBRV1 belongs to the genus Vesiculovirus. These observations suggest that both TRV and WBRV1 belong to a new genus of Rhabdoviridae. Next-generation genome sequencing of WBRV1 revealed 5 open reading frames of 1329, 765, 627, 1629, and 6336 bases in length. The WBRV1 gene sequences are similar to those of other rhabdoviruses. Epizootiological analysis of a population of wild boars in Wakayama prefecture in Japan indicated that 6.5% were positive for the WBRV1 gene and 52% were positive for WBRV1-neutralizing antibodies. Furthermore, such viral neutralizing antibodies were found in domestic pigs in another prefecture. WBRV1 was inoculated intranasally and intraperitoneally into SCID and BALB/c mice and viral RNA was detected in SCID mice, suggesting that WBRV1 can replicate in immunocompromised mice. These results indicate this novel virus is endemic in wild animals and livestock in Japan.
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Affiliation(s)
- Kouji Sakai
- Department of Virology 3, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Katsuro Hagiwara
- Virus Unit, School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Tsutomu Omatsu
- Research and Education center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Chinami Hamasaki
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
| | - Ryusei Kuwata
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
| | - Hiroshi Shimoda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
| | - Kazuo Suzuki
- Hikiiwa Park Center, 1629 Inari-cho, Tanabe 646-0051, Japan
| | - Daiji Endoh
- Department of Veterinary Radiology, School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu-shi 069-8501, Japan
| | - Noriyo Nagata
- Department of Pathology, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Makoto Nagai
- Research and Education center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Yukie Katayama
- Research and Education center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Mami Oba
- Research and Education center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Ichiro Kurane
- Department of Virology 1, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Masayuki Saijo
- Department of Virology 1, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Shigeru Morikawa
- Department of Veterinary Science, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 162-8640, Japan
| | - Tetsuya Mizutani
- Research and Education center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.
| | - Ken Maeda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan.
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Woo PCY, Lau SKP, Teng JLL, Tsang AKL, Joseph M, Wong EYM, Tang Y, Sivakumar S, Bai R, Wernery R, Wernery U, Yuen KY. Metagenomic analysis of viromes of dromedary camel fecal samples reveals large number and high diversity of circoviruses and picobirnaviruses. Virology 2014; 471-473:117-25. [PMID: 25461537 PMCID: PMC7112128 DOI: 10.1016/j.virol.2014.09.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 08/15/2014] [Accepted: 09/23/2014] [Indexed: 12/20/2022]
Abstract
The recent discovery of Middle East Respiratory Coronavirus and another novel dromedary camel coronavirus UAE-HKU23 in dromedaries has boosted interest in search of novel viruses in dromedaries. In this study, fecal samples of 203 dromedaries in Dubai were pooled and deep sequenced. Among the 7330 assembled viral contigs, 1970 were assigned to mammalian viruses. The largest groups of these contigs matched to Picobirnaviridae, Circoviridae, Picornaviridae, Parvoviridae, Astroviridae and Hepeviridae. Many of these viral families were previously unknown to dromedaries. In addition to the high abundance of contigs from Circoviridae (n=598 with 14 complete genomes) and Picobirnaviridae (n=1236), a high diversity of contigs from these two families was found, with the 14 Circoviridae complete genomes forming at least five clusters and contigs from both genogroup I and genogroup II potentially novel picobirnaviruses. Further studies comparing the incidence of these viral families in healthy and sick dromedaries will reveal their pathogenic potential. The viromes of fecal samples from dromedaries in the Middle East were analyzed. Circoviridae and Picobirnaviridae are most abundant among the mammalian viruses. A high diversity of contigs from Circoviridae and Picobirnaviridae was observed.
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Affiliation(s)
- Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China.
| | - Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Jade L L Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Alan K L Tsang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Marina Joseph
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Emily Y M Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ying Tang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | | | - Ru Bai
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Renate Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates.
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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Coffey LL, Page BL, Greninger AL, Herring BL, Russell RC, Doggett SL, Haniotis J, Wang C, Deng X, Delwart EL. Enhanced arbovirus surveillance with deep sequencing: Identification of novel rhabdoviruses and bunyaviruses in Australian mosquitoes. Virology 2013; 448:146-58. [PMID: 24314645 DOI: 10.1016/j.virol.2013.09.026] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 09/06/2013] [Accepted: 09/28/2013] [Indexed: 01/22/2023]
Abstract
Viral metagenomics characterizes known and identifies unknown viruses based on sequence similarities to any previously sequenced viral genomes. A metagenomics approach was used to identify virus sequences in Australian mosquitoes causing cytopathic effects in inoculated mammalian cell cultures. Sequence comparisons revealed strains of Liao Ning virus (Reovirus, Seadornavirus), previously detected only in China, livestock-infecting Stretch Lagoon virus (Reovirus, Orbivirus), two novel dimarhabdoviruses, named Beaumont and North Creek viruses, and two novel orthobunyaviruses, named Murrumbidgee and Salt Ash viruses. The novel virus proteomes diverged by ≥ 50% relative to their closest previously genetically characterized viral relatives. Deep sequencing also generated genomes of Warrego and Wallal viruses, orbiviruses linked to kangaroo blindness, whose genomes had not been fully characterized. This study highlights viral metagenomics in concert with traditional arbovirus surveillance to characterize known and new arboviruses in field-collected mosquitoes. Follow-up epidemiological studies are required to determine whether the novel viruses infect humans.
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Affiliation(s)
- Lark L Coffey
- Blood Systems Research Institute, University of California, San Francisco, USA; Department of Laboratory Medicine, University of California, 270 Masonic Avenue, San Francisco, CA 94118, USA
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