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Nayaka SN, Mondal F, Ranjan JK, Roy A, Mandal B. Bottle gourd IC-0262269, a super-susceptible genotype to tomato leaf curl Palampur virus. 3 Biotech 2024; 14:8. [PMID: 38074288 PMCID: PMC10709538 DOI: 10.1007/s13205-023-03838-y] [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: 07/10/2023] [Accepted: 10/29/2023] [Indexed: 01/19/2024] Open
Abstract
While conducting field trial of 82 genotypes of bottle gourd at Delhi during 2020-2021, a particular genotype, IC-0262269 was found to be affected by chlorotic curly stunt disease (CCSD). The affected plants were severely stunted and bearing very small chlorotic and crinkle leaves. The disease incidence in the said genotype was as high as 80% among different replicated trial blocks. The application of PCR using a generic primers specific to begomoviruses, as well as species-specific PCR diagnostics to six tomato-infecting begomoviruses: tomato leaf curl New Delhi virus (ToLCNDV), tomato leaf curl Palampur virus (ToLCPalV), tomato leaf curl Joydebpur virus (ToLCJoV), tomato leaf curl Gujrat virus (ToLCGuV), tomato leaf curl Bangalore virus (ToLCBV), and chilli leaf curl virus (ChiLCV) showed that, only ToLCPalV could be detected in the genotype IC-0262269. Following, rolling circle amplification, cloning and sequencing of full-length DNA-A and DNA-B genome of an isolate BoG1-ND from the genotype IC-0262269 revealed association of ToLCPalV with the disease. The successful agro-infection of the cloned genome of BoG1-ND (DNA-A and DNA-B) in the plants of Nicotiana benthamiana and bottle gourd demonstrated that ToLCPalV is the causal begomovirus of CCSD. The study provides the first evidence of the natural occurrence of ToLCPalV in bottle gourd crop and also showed that the bottle gourd genotype IC-0262269 is super-susceptible to ToLCPalV. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03838-y.
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Affiliation(s)
- S. Naveen Nayaka
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Firoz Mondal
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jeetendra Kumar Ranjan
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anirban Roy
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Bikash Mandal
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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2
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Jones A, Zhang D, Massey SE, Deigin Y, Nemzer LR, Quay SC. Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.12.528210. [PMID: 36865340 PMCID: PMC9979991 DOI: 10.1101/2023.02.12.528210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
HKU4-related coronaviruses are a group of betacoronaviruses belonging to the same merbecovirus subgenus as Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV), which causes severe respiratory illness in humans with a mortality rate of over 30%. The high genetic similarity between HKU4-related coronaviruses and MERS-CoV makes them an attractive subject of research for modeling potential zoonotic spillover scenarios. In this study, we identify a novel coronavirus contaminating agricultural rice RNA sequencing datasets from Wuhan, China. The datasets were generated by the Huazhong Agricultural University in early 2020. We were able to assemble the complete viral genome sequence, which revealed that it is a novel HKU4-related merbecovirus. The assembled genome is 98.38% identical to the closest known full genome sequence, Tylonycteris pachypus bat isolate BtTp-GX2012. Using in silico modeling, we identified that the novel HKU4-related coronavirus spike protein likely binds to human dipeptidyl peptidase 4 (DPP4), the receptor used by MERS-CoV. We further identified that the novel HKU4-related coronavirus genome has been inserted into a bacterial artificial chromosome in a format consistent with previously published coronavirus infectious clones. Additionally, we have found a near complete read coverage of the spike gene of the MERS-CoV reference strain HCoV-EMC/2012, and identify the likely presence of a HKU4-related-MERS chimera in the datasets. Our findings contribute to the knowledge of HKU4-related coronaviruses and document the use of a previously unpublished HKU4 reverse genetics system in apparent MERS-CoV related gain-of-function research. Our study also emphasizes the importance of improved biosafety protocols in sequencing centers and coronavirus research facilities.
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Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic. Nat Commun 2022; 13:2314. [PMID: 35538057 PMCID: PMC9090925 DOI: 10.1038/s41467-022-29614-9] [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: 11/12/2021] [Accepted: 02/28/2022] [Indexed: 01/08/2023] Open
Abstract
The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from Europe and the first from samples prior to the autumn peak. 1918 IAV genomic diversity is consistent with a combination of local transmission and long-distance dispersal events. Comparison of genomes before and during the pandemic peak shows variation at two sites in the nucleoprotein gene associated with resistance to host antiviral response, pointing at a possible adaptation of 1918 IAV to humans. Finally, local molecular clock modeling suggests a pure pandemic descent of seasonal H1N1 IAV as an alternative to the hypothesis of origination through an intrasubtype reassortment. For archival pathogens, like pH1N1 Influenza A virus the causative agent of 1918/19 pandemic, only few whole genome sequences exist. Here, Patrono et al. provide one complete and two partial genomes from Germany and find variation in two sites in the nucleoprotein gene in pandemic samples compared to pre-pandemic samples, that are associated with resistance to host antiviral response, pointing at a possible viral adaptation to humans.
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Genomic stratification and differential natural selection signatures among human norovirus genogroup II isolates. Arch Virol 2022; 167:1235-1245. [PMID: 35322317 PMCID: PMC8942050 DOI: 10.1007/s00705-022-05396-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/12/2022] [Indexed: 11/27/2022]
Abstract
Noroviruses (NoVs), which are members of the family Caliciviridae, are the most common cause of gastroenteritis in humans. Ten NoV genogroups have been reported so far. Of these, genogroup II (GII) is the most prevalent, and it causes serious infections worldwide. The complete genome sequences of NoV GII isolates from different geographical regions were retrieved from the public database. The model-based clustering approach, implemented in the STRUCTURE resource, was employed for assessment of genetic composition. The MEGA X and IQ Tree tools were used for phylogenetic analysis. Genome-wide natural selection analysis was performed using maximum-likelihood-based methods. The demographic features of NoV GII genome sequences were assessed using the BEAST package. All of the NoV GII sequences initially clustered into two main subpopulations at significant K = 2, where the genotype GII.4 samples clearly split from the rest of the genotypes. This indicates a marked genetic distinction between norovirus GII.4 and non-GII.4 samples. Phylogenetic analysis showed the presence of five distinct subclades for genotype GII.2 and seven subclades for GII.4 samples. Several isolates with admixed ancestry were identified that constituted distinct subclusters in the phylogenetic tree. No continental-specific genetic distinctions were observed among the NoV GII samples. Significant genomic signatures of both positive and negative natural selection were identified across the NoV GII genes. A differential pattern of positive selection signals was inferred between the GII.4 and non-GII.4 genotypes. The demographic analysis revealed an increase in the effective population size of NoV GII during 2009-2010, followed by a rapid fall in 2015.
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Shin MD, Shukla S, Chung YH, Beiss V, Chan SK, Ortega-Rivera OA, Wirth DM, Chen A, Sack M, Pokorski JK, Steinmetz NF. COVID-19 vaccine development and a potential nanomaterial path forward. NATURE NANOTECHNOLOGY 2020; 15:646-655. [PMID: 32669664 DOI: 10.1038/s41565-020-0737-y] [Citation(s) in RCA: 398] [Impact Index Per Article: 99.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 05/18/2023]
Abstract
The COVID-19 pandemic has infected millions of people with no clear signs of abatement owing to the high prevalence, long incubation period and lack of established treatments or vaccines. Vaccines are the most promising solution to mitigate new viral strains. The genome sequence and protein structure of the 2019-novel coronavirus (nCoV or SARS-CoV-2) were made available in record time, allowing the development of inactivated or attenuated viral vaccines along with subunit vaccines for prophylaxis and treatment. Nanotechnology benefits modern vaccine design since nanomaterials are ideal for antigen delivery, as adjuvants, and as mimics of viral structures. In fact, the first vaccine candidate launched into clinical trials is an mRNA vaccine delivered via lipid nanoparticles. To eradicate pandemics, present and future, a successful vaccine platform must enable rapid discovery, scalable manufacturing and global distribution. Here, we review current approaches to COVID-19 vaccine development and highlight the role of nanotechnology and advanced manufacturing.
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Affiliation(s)
- Matthew D Shin
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - Sourabh Shukla
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - Young Hun Chung
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Veronique Beiss
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - Soo Khim Chan
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - Oscar A Ortega-Rivera
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - David M Wirth
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - Angela Chen
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | | | - Jonathan K Pokorski
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
- Center for Nano-ImmunoEngineering, University of California San Diego, La Jolla, CA, USA
- Institute for Materials Discovery and Design, University of California San Diego, La Jolla, CA, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Center for Nano-ImmunoEngineering, University of California San Diego, La Jolla, CA, USA.
- Institute for Materials Discovery and Design, University of California San Diego, La Jolla, CA, USA.
- Department of Radiology, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
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Wokorach G, Otim G, Njuguna J, Edema H, Njung'e V, Machuka EM, Yao N, Stomeo F, Echodu R. Genomic analysis of Sweet potato feathery mottle virus from East Africa. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY 2020; 110:101473. [PMID: 32454559 PMCID: PMC7233136 DOI: 10.1016/j.pmpp.2020.101473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 06/11/2023]
Abstract
Sweet potato feathery mottle virus is a potyvirus that infect sweet potato. The genome of the virus was analysed to understand genetic diversity, evolution and gene flow. Motifs, nucleotide identity and a phylogenetic tree were used to determine phylogroup of the isolates. Gene flow and genetic diversity were tested using DnaSP v.5. Codons evolution were tested using three methods embedded in Datamonkey. The results indicate occurrence of an isolate of phylogroup B within East Africa. Low genetic differentiation was observed between isolates from Kenya and Uganda indicating evidence of gene flow between the two countries. Four genes were found to have positively selected codons bordering or occurring within functional motifs. A motif within P1 gene evolved differently between phylogroup A and B. The evidence of gene flow indicates frequent exchange of the virus between the two countries and P1 gene motif provide a possible marker that can be used for mapping the distribution of the phylogroups.
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Affiliation(s)
- Godfrey Wokorach
- Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda
| | - Geoffrey Otim
- Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda
- Faculty of Agriculture, Gulu University, P.O. Box 166, Gulu, Uganda
| | - Joyce Njuguna
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Hilary Edema
- Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda
| | - Vincent Njung'e
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Eunice M. Machuka
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Nasser Yao
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Richard Echodu
- Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda
- Faculty of Agriculture, Gulu University, P.O. Box 166, Gulu, Uganda
- Department of Biology, Faculty of Science, Gulu University, P.O. Box 166, Gulu, Uganda
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7
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Detection and characterization of a novel hepacivirus in long-tailed ground squirrels (Spermophilus undulatus) in China. Arch Virol 2019; 164:2401-2410. [PMID: 31243554 DOI: 10.1007/s00705-019-04303-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 05/02/2019] [Indexed: 12/13/2022]
Abstract
Rodent populations are known to be reservoirs of viruses with the potential to infect humans. However, a large number of such viruses remain undiscovered. In this study, we investigated the shedding of unknown viruses in long-tailed ground squirrel (Spermophilus undulatus) feces by high-throughput sequencing. A novel and highly divergent virus related to members of the genus Hepacivirus was identified in ground squirrel liver. This virus, tentatively named RHV-GS2015, was found to have a genome organization that is typical of hepaciviruses, including a long open reading frame encoding a polyprotein of 2763 aa. Sequence alignment of RHV-GS2015 with the most closely related hepaciviruses yielded p-distances of the NS3 and NS5B regions of 0.546 and 0.476, respectively, supporting the conclusion that RHV-GS2015 is a member of a new hepacivirus species, which we propose to be named "Hepacivirus P". Phylogenetic analysis of the NS3 and NS5B regions indicated that RHV-GS2015 shares common ancestry with other rodent hepaciviruses (species Hepacivirus E, and species Hepacivirus F), Norway rat hepacivirus 1 (species Hepacivirus G), and Norway rat hepacivirus 2 (species Hepacivirus H). A phylogenetic tree including the seven previously identified rodent hepaciviruses revealed extreme genetic heterogeneity among these viruses. RHV-GS2015 was detected in 7 out of 12 ground squirrel pools and was present in liver, lung, and spleen tissues. Furthermore, livers showed extremely high viral loads of RHV-GS2015, ranging from 2.5 × 106 to 2.0 × 108 copies/g. It is reasonable to assume that this novel virus is hepatotropic, like hepatitis C virus. The discovery of RHV-GS2015 extends our knowledge of the genetic diversity and host range of hepaciviruses, helping to elucidate their origins and evolution.
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8
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A genome-wide diversity study of grapevine rupestris stem pitting-associated virus. Arch Virol 2018; 163:3105-3111. [DOI: 10.1007/s00705-018-3945-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 05/14/2018] [Indexed: 10/28/2022]
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9
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Gerba CP, Betancourt WQ, Kitajima M. How much reduction of virus is needed for recycled water: A continuous changing need for assessment? WATER RESEARCH 2017; 108:25-31. [PMID: 27838026 PMCID: PMC7112101 DOI: 10.1016/j.watres.2016.11.020] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 05/10/2023]
Abstract
To ensure the safety of wastewater reuse for irrigation of food crops and drinking water pathogenic viruses must be reduced to levels that pose no significant risk. To achieve this goal minimum reduction of viruses by treatment trains have been suggested. For use of edible crops a 6-log reduction and for production of potable drinking water a 12-log reduction has been suggested. These reductions were based on assuming infective virus concentrations of 105 to 106 per liter. Recent application of molecular methods suggests that some pathogenic viruses may be occurring in concentrations of 107 to 109 per liter. Factors influencing these levels include the development of molecular methods for virus detection, emergence of newly recognized viruses, decrease in per capita water use due to conservation measures, and outbreaks. Since neither cell culture nor molecular methods can assess all the potentially infectious virus in wastewater conservative estimates should be used to assess the virus load in untreated wastewater. This review indicates that an additional 2- to 3-log reduction of viruses above current recommendations may be needed to ensure the safety of recycled water. Information is needed on peak loading of viruses. In addition, more virus groups need to be quantified using better methods of virus quantification, including more accurate methods for measuring viral infectivity in order to better quantify risks from viruses in recycled water.
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Affiliation(s)
- Charles P Gerba
- The Water, Energy and Sustainable Technology Center, Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, United States.
| | - Walter Q Betancourt
- The Water, Energy and Sustainable Technology Center, Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, United States.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan.
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Kiss I, Mató T, Homonnay Z, Tatár-Kis T, Palya V. Successive occurrence of recombinant infectious bronchitis virus strains in restricted area of Middle East. Virus Evol 2016; 2:vew021. [PMID: 29492274 PMCID: PMC5822880 DOI: 10.1093/ve/vew021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Routine molecular diagnostic testing by our laboratory, based on using a primer pair with conservative binding sites on the spike glycoprotein coding sequence, has indicated the recurring of a unique phylogenetic cluster of chicken infectious bronchitis viruses (IBV) in the Middle East since 2010. The nearly full-length S1 subunit of the spike gene phylogeny of selected strains, however, split up this grouping, suggesting potential recombination in the S1 gene. In order to clarify this, various bioinformatic analyses of the strains were carried out, which confirmed this supposition. Two patterns of recombination were found among the strains, one of which could also be identified in GenBank-deposited IBV sequences from the region. These findings demonstrate that IBV strains of different recombinant patterns occur simultaneously in the same geographic region and could circulate for an extended period of time, thus contributing to the knowledge on IBV evolution.
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Affiliation(s)
- István Kiss
- Scientific Support and Investigation Unit, Ceva-Phylaxia, Szállás u. 5, Budapest 1107, Hungary
| | - Tamás Mató
- Scientific Support and Investigation Unit, Ceva-Phylaxia, Szállás u. 5, Budapest 1107, Hungary
| | - Zalán Homonnay
- Scientific Support and Investigation Unit, Ceva-Phylaxia, Szállás u. 5, Budapest 1107, Hungary
| | - Tímea Tatár-Kis
- Scientific Support and Investigation Unit, Ceva-Phylaxia, Szállás u. 5, Budapest 1107, Hungary
| | - Vilmos Palya
- Scientific Support and Investigation Unit, Ceva-Phylaxia, Szállás u. 5, Budapest 1107, Hungary
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Wickramaarachchi WART, Shankarappa KS, Rangaswamy KT, Maruthi MN, Rajapakse RGAS, Ghosh S. Molecular characterization of banana bunchy top virus isolate from Sri Lanka and its genetic relationship with other isolates. Virusdisease 2016; 27:154-60. [PMID: 27366766 DOI: 10.1007/s13337-016-0311-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/08/2016] [Indexed: 10/22/2022] Open
Abstract
Bunchy top disease of banana caused by Banana bunchy top virus (BBTV, genus Babuvirus family Nanoviridae) is one of the most important constraints in production of banana in the different parts of the world. Six genomic DNA components of BBTV isolate from Kandy, Sri Lanka (BBTV-K) were amplified by polymerase chain reaction (PCR) with specific primers using total DNA extracted from banana tissues showing typical symptoms of bunchy top disease. The amplicons were of expected size of 1.0-1.1 kb, which were cloned and sequenced. Analysis of sequence data revealed the presence of six DNA components; DNA-R, DNA-U3, DNA-S, DNA-N, DNA-M and DNA-C for Sri Lanka isolate. Comparisons of sequence data of DNA components followed by the phylogenetic analysis, grouped Sri Lanka-(Kandy) isolate in the Pacific Indian Oceans (PIO) group. Sri Lanka-(Kandy) isolate of BBTV is classified a new member of PIO group based on analysis of six components of the virus.
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Affiliation(s)
- W A R T Wickramaarachchi
- Division of Plant Pathology, Department of Agriculture, Horticulture Crops Research and Development Institute, Gannoruwa, Peradeniya, 20400 Sri Lanka
| | - K S Shankarappa
- Department of Plant Pathology, K. R. C. College of Horticulture, Arabhavi, University of Horticultural Sciences, Bagalkot, Karnataka India
| | - K T Rangaswamy
- Department of Plant Pathology, University of Agricultural Sciences, GKVK, Bengaluru, 560 065 India
| | - M N Maruthi
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB UK
| | - R G A S Rajapakse
- Division of Plant Pathology, Department of Agriculture, Horticulture Crops Research and Development Institute, Gannoruwa, Peradeniya, 20400 Sri Lanka
| | - Saptarshi Ghosh
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB UK
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Lu L, Van Dung N, Bryant JE, Carrique-Mas J, Van Cuong N, Anh PH, Rabaa MA, Baker S, Simmonds P, Woolhouse ME. Evolution and phylogeographic dissemination of endemic porcine picornaviruses in Vietnam. Virus Evol 2016; 2:vew001. [PMID: 27774295 PMCID: PMC4989877 DOI: 10.1093/ve/vew001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Members of the Picornaviridae are important and often zoonotic viruses responsible for a variety of human and animal diseases. However, the evolution and spatial dissemination of different picornaviruses circulating in domestic animals are not well studied. We examined the rate of evolution and time of origin of porcine enterovirus G (EV-G) and porcine kobuvirus species C lineages (PKV-C) circulating in pig farms in Vietnam and from other countries. We further explored the spatiotemporal spread of EV-G and PKV-C in Southwest Vietnam using phylogeographic models. Multiple types of EV-G are co-circulating in Vietnam. The two dominant EV-G types among isolates from Vietnam (G1 and G6) showed strong phylogenetic clustering. Three clades of PKV-C (PKV-C1-3) represent more recent introductions into Vietnam; PKV-C2 is closely related to PKV-C from Southwest China, indicating possible cross-border dissemination. In addition, high virus lineage migration rates were estimated within four districts in Dong Thap province in Vietnam for both EV-G types (G1, G6) and all PKV-C (C1-3) clades. We found that Chau Thanh district is a primary source of both EV-G and PKV-C clades, consistent with extensive pig trading in and out of the district. Understanding the evolution and spatial dissemination of endemic picornaviruses in pigs may inform future strategies for the surveillance and control of picornaviruses.
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Affiliation(s)
- Lu Lu
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Nguyen Van Dung
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam,; Nuffield Department of Medicine, Oxford University, Old Rd, Oxford OX3 7LF, UK and
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Pham Honh Anh
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam,; Nuffield Department of Medicine, Oxford University, Old Rd, Oxford OX3 7LF, UK and; The London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT, UK
| | - Peter Simmonds
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK,; Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Mark E Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
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13
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The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin. Arch Virol 2016; 161:959-66. [PMID: 26780893 DOI: 10.1007/s00705-016-2756-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/08/2016] [Indexed: 01/14/2023]
Abstract
Viral metagenomics of feces collected from 58 Peruvian children with unexplained diarrhea revealed several small circular ssDNA genomes. Two genomes related to sequences previously reported in feces from chimpanzees and other mammals and recently named smacoviruses were characterized and then detected by PCR in 1.7 % (1/58) and 19 % (11/58) of diarrheal samples, respectively. Another three genomes from a distinct small circular ssDNA viral group provisionally called pecoviruses encoded Cap and Rep proteins with <35 % identity to those in related genomes reported in human, seal, porcine and dromedary feces. Pecovirus DNA was detected in 15.5 % (9/58), 5.9 % (3/51) and 3 % (3/100) of fecal samples from unexplained diarrhea in Peru, Nicaragua and Chile, respectively. Feces containing these ssDNA genomes also contained known human enteric viral pathogens. The cellular origins of these circular ssDNA viruses, whether human cells, ingested plants, animals or fungal foods, or residents of the gut microbiome, are currently unknown.
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