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An N, Wu Q, Fang Z, Xiang L, Liu Q, Tan L, Weng Q. Genome analysis and classification of Xanthomonas bacteriophage AhaSv, a new member of the genus Salvovirus. Arch Virol 2024; 169:117. [PMID: 38739272 DOI: 10.1007/s00705-024-06047-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024]
Abstract
Xanthomonas phage AhaSv was isolated from lake water. Genome sequencing showed that its genome is a linear dsDNA molecule with a length of 55,576 bp and a G+C content of 63.23%. Seventy-one open reading frames (ORFs) were predicted, and no tRNAs were found in the genome. Phylogenetic analysis showed that AhaSv is closely related to members of the genus Salvovirus of the family Casjensviridae. Intergenomic similarity values between phage AhaSv and homologous phages were up to 90.6%, suggesting that phage AhaSv should be considered a member of a new species in the genus Salvovirus.
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Affiliation(s)
- Ni An
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Lan Xiang
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China.
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China.
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2
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Zheng Y, Gao Z, Wu S, Ruan A. Community Structure, Drivers, and Potential Functions of Different Lifestyle Viruses in Chaohu Lake. Viruses 2024; 16:590. [PMID: 38675931 PMCID: PMC11053968 DOI: 10.3390/v16040590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Viruses, as the most prolific entities on Earth, constitute significant ecological groups within freshwater lakes, exerting pivotal ecological roles. In this study, we selected Chaohu Lake, a representative eutrophic freshwater lake in China, as our research site to explore the community distribution, driving mechanisms, and potential ecological functions of diverse viral communities, the intricate virus-host interaction systems, and the overarching influence of viruses on global biogeochemical cycling.
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Affiliation(s)
- Yu Zheng
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Zihao Gao
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Shuai Wu
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Aidong Ruan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Geography and Remote Sensing, Hohai University, Nanjing 210098, China
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3
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Niner MD, Stepien CA, Gorgoglione B, Leaman DW. Genomic and immunogenic changes of Piscine novirhabdovirus (Viral Hemorrhagic Septicemia Virus) over its evolutionary history in the Laurentian Great Lakes. PLoS One 2021; 16:e0232923. [PMID: 34048438 PMCID: PMC8162641 DOI: 10.1371/journal.pone.0232923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/22/2021] [Indexed: 01/21/2023] Open
Abstract
A unique and highly virulent subgenogroup (-IVb) of Piscine novirhabdovirus, also known as Viral Hemorrhagic Septicemia Virus (VHSV), suddenly appeared in the Laurentian Great Lakes, causing large mortality outbreaks in 2005 and 2006, and affecting >32 freshwater fish species. Periods of apparent dormancy have punctuated smaller and more geographically-restricted outbreaks in 2007, 2008, and 2017. In this study, we conduct the largest whole genome sequencing analysis of VHSV-IVb to date, evaluating its evolutionary changes from 48 isolates in relation to immunogenicity in cell culture. Our investigation compares genomic and genetic variation, selection, and rates of sequence changes in VHSV-IVb, in relation to other VHSV genogroups (VHSV-I, VHSV-II, VHSV-III, and VHSV-IVa) and with other Novirhabdoviruses. Results show that the VHSV-IVb isolates we sequenced contain 253 SNPs (2.3% of the total 11,158 nucleotides) across their entire genomes, with 85 (33.6%) of them being non-synonymous. The most substitutions occurred in the non-coding region (NCDS; 4.3%), followed by the Nv- (3.8%), and M- (2.8%) genes. Proportionally more M-gene substitutions encoded amino acid changes (52.9%), followed by the Nv- (50.0%), G- (48.6%), N- (35.7%) and L- (23.1%) genes. Among VHSV genogroups and subgenogroups, VHSV-IVa from the northeastern Pacific Ocean has shown the fastest substitution rate (2.01x10-3), followed by VHSV-IVb (6.64x10-5) and by the VHSV-I, -II and-III genogroups from Europe (4.09x10-5). A 2016 gizzard shad (Dorosoma cepedianum) from Lake Erie possessed the most divergent VHSV-IVb sequence. The in vitro immunogenicity analysis of that sample displayed reduced virulence (as did the other samples from 2016), in comparison to the original VHSV-IVb isolate (which had been traced back to 2003, as an origin date). The 2016 isolates that we tested induced milder impacts on fish host cell innate antiviral responses, suggesting altered phenotypic effects. In conclusion, our overall findings indicate that VHSV-IVb has undergone continued sequence change and a trend to lower virulence over its evolutionary history (2003 through present-day), which may facilitate its long-term persistence in fish host populations.
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Affiliation(s)
- Megan D. Niner
- Department of Environmental Sciences, University of Toledo, Toledo, Ohio, United States of America
| | - Carol A. Stepien
- School of Oceanography, University of Washington, Seattle, WA, United States of America
- Genetics and Genomics Group, NOAA Pacific Marine Environmental Laboratory, Seattle, Washington, United States of America
- * E-mail: ,
| | - Bartolomeo Gorgoglione
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, United States of America
| | - Douglas W. Leaman
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, United States of America
- Department of Biological Sciences, Wright State University, Dayton, Ohio, United States of America
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Opere WM, John M, Ombori O. Molecular Detection of Human Enteric Adenoviruses in Water Samples Collected from Lake Victoria Waters Along Homa Bay Town, Homa Bay County, Kenya. Food Environ Virol 2021; 13:32-43. [PMID: 33141920 DOI: 10.1007/s12560-020-09444-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Lake Victoria is the primary source of water for millions of people in the Sub-Saharan Africa region. In recent years, population development around the lake has resulted in compromised sanitation standards resulting in increased faecal pollution of the lake. Consequently, this condition has increased the chances of waterborne enteric viruses, such as adenoviruses' circulation in the community. Adenoviruses can affect health in both humans and animals by causing a myriad of diseases including the gastrointestinal infections. The study aimed to detect contamination of the lake water with pathogenic human adenoviruses along Homa Bay town, Homa Bay County, Kenya. To examine the presence of adenoviral genome, we collected a total of 216 (monthly n = 36) water samples from six different locations marked by high levels of anthropogenic activities along the shoreline. Molecular amplification technique using the nested PCR procedure was used to detect the genomes from the water samples. Human adenoviruses were detected in 11 samples (5.09%). Statistical analyses indicated a significant correlation between adenovirus presence and the approximate distance from pit latrines and sewage treatment works at the area. The findings indicate that faecal contamination of the lake waters originated from the point sources. The findings also suggest a possibility of elevated levels of faecal pollution in different surface waters within the lake basin. The findings indicate that some of the enteric viruses circulating in the local community are human adenovirus type 40, and 41. The data may provide a basis for recognizing the need to prioritize environmental monitoring for enteric virus contamination on an on-going basis.
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Affiliation(s)
- Wasonga Michael Opere
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P.O. Box 43844-00100, Nairobi, Kenya.
| | - Maingi John
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P.O. Box 43844-00100, Nairobi, Kenya
| | - Omwoyo Ombori
- Department of Plant Sciences, Kenyatta University, P.O. Box 43844-00100, Nairobi, Kenya
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McKindles KM, Manes MA, DeMarco JR, McClure A, McKay RM, Davis TW, Bullerjahn GS. Dissolved Microcystin Release Coincident with Lysis of a Bloom Dominated by Microcystis spp. in Western Lake Erie Attributed to a Novel Cyanophage. Appl Environ Microbiol 2020; 86:e01397-20. [PMID: 32859600 PMCID: PMC7642080 DOI: 10.1128/aem.01397-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/25/2020] [Indexed: 11/20/2022] Open
Abstract
Western Lake Erie (Laurentian Great Lakes) is prone to annual cyanobacterial harmful algal blooms (cHABs) dominated by Microcystis spp. that often yield microcystin toxin concentrations exceeding the federal EPA recreational contact advisory of 8 μg liter-1 In August 2014, microcystin levels were detected in finished drinking water above the World Health Organization 1.0 μg liter-1 threshold for consumption, leading to a 2-day disruption in the supply of drinking water for >400,000 residents of Toledo, Ohio (USA). Subsequent metatranscriptomic analysis of the 2014 bloom event provided evidence that release of toxin into the water supply was likely caused by cyanophage lysis that transformed a portion of the intracellular microcystin pool into the dissolved fraction, rendering it more difficult to eliminate during treatment. In August 2019, a similar increase in dissolved microcystins at the Toledo water intake was coincident with a viral lytic event caused by a phage consortium different in composition from what was detected following the 2014 Toledo water crisis. The most abundant viral sequence in metagenomic data sets was a scaffold from a putative member of the Siphoviridae, distinct from the Ma-LMM01-like Myoviridae that are typically documented to occur in western Lake Erie. This study provides further evidence that viral activity in western Lake Erie plays a significant role in transformation of microcystins from the particulate to the dissolved fraction and therefore requires monitoring efforts from local water treatment plants. Additionally, identification of multiple lytic cyanophages will enable the development of a quantitative PCR toolbox to assess viral activity during cHABs.IMPORTANCE Viral attack on cHABs may contribute to changes in community composition during blooms, as well as bloom decline, yet loss of bloom biomass does not eliminate the threat of cHAB toxicity. Rather, it may increase risks to the public by delivering a pool of dissolved toxin directly into water treatment utilities when the dominating Microcystis spp. are capable of producing microcystins. Detecting, characterizing, and quantifying the major cyanophages involved in lytic events will assist water treatment plant operators in making rapid decisions regarding the pool of microcystins entering the plant and the corresponding best practices to neutralize the toxin.
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Affiliation(s)
- Katelyn M McKindles
- Department of Biological Sciences and Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| | - Makayla A Manes
- Department of Biological Sciences and Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| | - Jonathan R DeMarco
- Department of Biological Sciences and Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| | - Andrew McClure
- Division of Water Treatment for the City of Toledo, Toledo, Ohio, USA
| | - R Michael McKay
- Department of Biological Sciences and Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - Timothy W Davis
- Department of Biological Sciences and Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
- Center for Great Lakes and Watershed Studies, Bowling Green State University, Bowling Green, Ohio, USA
| | - George S Bullerjahn
- Department of Biological Sciences and Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
- Center for Great Lakes and Watershed Studies, Bowling Green State University, Bowling Green, Ohio, USA
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Girard C, Langlois V, Vigneron A, Vincent WF, Culley AI. Seasonal Regime Shift in the Viral Communities of a Permafrost Thaw Lake. Viruses 2020; 12:v12111204. [PMID: 33105728 PMCID: PMC7690404 DOI: 10.3390/v12111204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 09/22/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022] Open
Abstract
Permafrost thaw lakes including thermokarst lakes and ponds are ubiquitous features of Subarctic and Arctic landscapes and are hotspots of microbial activity. Input of terrestrial organic matter into the planktonic microbial loop of these lakes may greatly amplify global greenhouse gas emissions. This microbial loop, dominated in the summer by aerobic microorganisms including phototrophs, is radically different in the winter, when metabolic processes shift to the anaerobic degradation of organic matter. Little is known about the viruses that infect these microbes, despite evidence that viruses can control microbial populations and influence biogeochemical cycling in other systems. Here, we present the results of a metagenomics-based study of viruses in the larger than 0.22 µm fraction across two seasons (summer and winter) in a permafrost thaw lake in Subarctic Canada. We uncovered 351 viral populations (vOTUs) in the surface waters of this lake, with diversity significantly greater during the summer. We also identified and characterized several phage genomes and prophages, which were mostly present in the summer. Finally, we compared the viral community of this waterbody to other habitats and found unexpected similarities with distant bog lakes in North America.
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Affiliation(s)
- Catherine Girard
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC G1V 0A6, Canada; (C.G.); (V.L.)
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
| | - Valérie Langlois
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC G1V 0A6, Canada; (C.G.); (V.L.)
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
| | - Adrien Vigneron
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Warwick F. Vincent
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Alexander I. Culley
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC G1V 0A6, Canada; (C.G.); (V.L.)
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
- Correspondence:
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7
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Abstract
A high number of viral metagenomes have revealed countless genomes of putative bacteriophages that have not yet been identified due to limitations in bacteriophage cultures. However, most virome studies have been focused on marine or gut environments, thereby leaving the viral community structure of freshwater lakes unclear. Because the lakes located around the globe have independent ecosystems with unique characteristics, viral community structures are also distinctive but comparable. Here, we present data on viral metagenomes that were seasonally collected at a depth of 1 m from Lake Soyang, the largest freshwater reservoir in South Korea. Through shotgun metagenome sequencing using the Illumina MiSeq platform, 3.08 to 5.54-Gbps of reads per virome were obtained. To predict the viral genome sequences within Lake Soyang, contigs were constructed and 648 to 1,004 putative viral contigs were obtained per sample. We expect that both viral metagenome reads and viral contigs would contribute in comparing and understanding of viral communities among different freshwater lakes depending on seasonal changes.
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Affiliation(s)
- Kira Moon
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Suhyun Kim
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Ilnam Kang
- Center for Molecular and Cell Biology, Inha University, Incheon, 22212, Republic of Korea.
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea.
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8
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Panwar P, Allen MA, Williams TJ, Hancock AM, Brazendale S, Bevington J, Roux S, Páez-Espino D, Nayfach S, Berg M, Schulz F, Chen IMA, Huntemann M, Shapiro N, Kyrpides NC, Woyke T, Eloe-Fadrosh EA, Cavicchioli R. Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community. Microbiome 2020; 8:116. [PMID: 32772914 PMCID: PMC7416419 DOI: 10.1186/s40168-020-00889-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/30/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Cold environments dominate the Earth's biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000-7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles. RESULTS The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts. CONCLUSION Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems. Video Abstract.
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Affiliation(s)
- Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Tasmania, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- , 476 Lancaster Rd, Pegarah, Australia
| | - James Bevington
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Simon Roux
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - David Páez-Espino
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Mammoth BioSciences, 279 East Grand Ave, South San Francisco, CA, USA
| | - Stephen Nayfach
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Maureen Berg
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - I-Min A Chen
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
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9
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Sellyei B, Baska F, Varga Á, Borzák R, Doszpoly A. Molecular detection of a novel cyprinid herpesvirus in roach (Rutilus rutilus) and asp (Leuciscus aspius) showing typical signs of carp pox disease. Arch Virol 2020; 165:1569-1576. [PMID: 32358627 PMCID: PMC7289782 DOI: 10.1007/s00705-020-04638-y] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/01/2020] [Indexed: 11/25/2022]
Abstract
In the early spring of 2018, in Lake Balaton (Hungary), a roach (Rutilus rutilus) and an asp (Leuciscus aspius) were found in an fish trap at the outlet of the river Sió showing typical signs of the so-called carp pox disease, such as foci of epidermal hyperplasia on the head and the whole body surface, including the fins. Molecular tests revealed the presence of the DNA of an unknown fish herpesvirus. Three genes encoding the DNA-dependent DNA polymerase, major capsid protein and ATPase subunit of terminase were amplified and sequenced from the alloherpesviral genome. The gene sequences of the viruses obtained from the two different fish species shared 94.4% nucleotide sequence identity (98.1% amino acid sequence identity), suggesting that they belong to the same virus species. Phylogenetic analysis based on the DNA polymerase (and the concatenated sequences of the amplified genes, as well) implied that the detected virus belongs to the genus Cyprinivirus within the family Alloherpesviridae. The sequences of the novel alloherpesvirus diverge from those of the five cyprinivirus species described previously, so it putatively represents the sixth virus species in the genus.
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Affiliation(s)
- Boglárka Sellyei
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, P.O. Box 18, Budapest, 1581, Hungary
| | - Ferenc Baska
- Department of Exotic Animal and Wildlife Medicine, University of Veterinary Medicine, Budapest, Hungary
| | - Ádám Varga
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, P.O. Box 18, Budapest, 1581, Hungary
| | - Réka Borzák
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, P.O. Box 18, Budapest, 1581, Hungary
| | - Andor Doszpoly
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, P.O. Box 18, Budapest, 1581, Hungary.
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Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, Castelle CJ, Olm MR, Bouma-Gregson K, Amano Y, He C, Méheust R, Brooks B, Thomas A, Lavy A, Matheus-Carnevali P, Sun C, Goltsman DSA, Borton MA, Sharrar A, Jaffe AL, Nelson TC, Kantor R, Keren R, Lane KR, Farag IF, Lei S, Finstad K, Amundson R, Anantharaman K, Zhou J, Probst AJ, Power ME, Tringe SG, Li WJ, Wrighton K, Harrison S, Morowitz M, Relman DA, Doudna JA, Lehours AC, Warren L, Cate JHD, Santini JM, Banfield JF. Clades of huge phages from across Earth's ecosystems. Nature 2020; 578:425-431. [PMID: 32051592 PMCID: PMC7162821 DOI: 10.1038/s41586-020-2007-4] [Citation(s) in RCA: 221] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 01/02/2020] [Indexed: 12/31/2022]
Abstract
Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.
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Affiliation(s)
- Basem Al-Shayeb
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Lin-Xing Chen
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Fred Ward
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Audra Devoto
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Cindy J Castelle
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Matthew R Olm
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Keith Bouma-Gregson
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai-mura, Japan
| | - Christine He
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Raphaël Méheust
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Brandon Brooks
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alex Thomas
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Adi Lavy
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | | | - Christine Sun
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | | | - Mikayla A Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Allison Sharrar
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Alexander L Jaffe
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Tara C Nelson
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Rose Kantor
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ray Keren
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Katherine R Lane
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ibrahim F Farag
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Shufei Lei
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Kari Finstad
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Ronald Amundson
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Karthik Anantharaman
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | | | - Alexander J Probst
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Mary E Power
- Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Kelly Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Sue Harrison
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Michael Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - David A Relman
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Anne-Catherine Lehours
- Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
| | - Lesley Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Jamie H D Cate
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA.
- School of Earth Sciences, University of Melbourne, Melbourne, Victoria, Australia.
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11
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McMinn BR, Rhodes ER, Huff EM, Korajkic A. Decay of infectious adenovirus and coliphages in freshwater habitats is differentially affected by ambient sunlight and the presence of indigenous protozoa communities. Virol J 2020; 17:1. [PMID: 31906972 PMCID: PMC6945520 DOI: 10.1186/s12985-019-1274-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/17/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Sanitary quality of recreational waters worldwide is assessed using fecal indicator bacteria (FIB), such as Escherichia coli and enterococci. However, fate and transport characteristics of FIB in aquatic habitats can differ from those of viral pathogens which have been identified as main etiologic agents of recreational waterborne illness. Coliphages (bacteriophages infecting E. coli) are an attractive alternative to FIB because of their many morphological and structural similarities to viral pathogens. METHODS In this in situ field study, we used a submersible aquatic mesocosm to compare decay characteristics of somatic and F+ coliphages to those of infectious human adenovirus 2 in a freshwater lake. In addition, we also evaluated the effect of ambient sunlight (and associated UV irradiation) and indigenous protozoan communities on decay of somatic and F+ coliphage, as well as infectious adenovirus. RESULTS Our results show that decay of coliphages and adenovirus was similar (p = 0.0794), indicating that both of these bacteriophage groups are adequate surrogates for decay of human adenoviruses. Overall, after 8 days the greatest log10 reductions were observed when viruses were exposed to a combination of biotic and abiotic factors (2.92 ± 0.39, 4.48 ± 0.38, 3.40 ± 0.19 for somatic coliphages, F+ coliphages and adenovirus, respectively). Both, indigenous protozoa and ambient sunlight, were important contributors to decay of all three viruses, although the magnitude of that effect differed over time and across viral targets. CONCLUSIONS While all viruses studied decayed significantly faster (p < 0.0001) when exposed to ambient sunlight, somatic coliphages were particularly susceptible to sunlight irradiation suggesting a potentially different mechanism of UV damage compared to F+ coliphages and adenoviruses. Presence of indigenous protozoan communities was also a significant contributor (p value range: 0.0016 to < 0.0001) to decay of coliphages and adenovirus suggesting that this rarely studied biotic factor is an important driver of viral reductions in freshwater aquatic habitats.
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Affiliation(s)
- Brian R McMinn
- United States Environmental Protections Agency, Cincinnati, OH, 45268, USA
| | - Eric R Rhodes
- United States Environmental Protections Agency, Cincinnati, OH, 45268, USA
| | - Emma M Huff
- United States Environmental Protections Agency, Cincinnati, OH, 45268, USA
| | - Asja Korajkic
- United States Environmental Protections Agency, Cincinnati, OH, 45268, USA.
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12
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Ruiz-Perez CA, Tsementzi D, Hatt JK, Sullivan MB, Konstantinidis KT. Prevalence of viral photosynthesis genes along a freshwater to saltwater transect in Southeast USA. Environ Microbiol Rep 2019; 11:672-689. [PMID: 31265211 DOI: 10.1111/1758-2229.12780] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 06/29/2019] [Indexed: 05/28/2023]
Abstract
Bacteriophages encode host-acquired functional genes known as auxiliary metabolic genes (AMGs). Photosynthesis AMGs are commonly found in marine cyanobacteria-infecting Myoviridae and Podoviridae cyanophages, but their ecology remains understudied in freshwater environments. To advance knowledge of this issue, we analysed viral metagenomes collected in the summertime for four years from five lakes and two estuarine locations interconnected by the Chattahoochee River, Southeast USA. Sequences representing ten different AMGs were recovered and found to be prevalent in all sites. Most freshwater AMGs were 10-fold less abundant than estuarine and marine AMGs and were encoded by novel Myoviridae and Podoviridae cyanophage genera. Notably, several of the corresponding viral genomes showed endemism to a specific province along the river. This translated into psbA gene phylogenetic clustering patterns that matched a marine vs. freshwater origin indicating that psbA may serve as a robust classification and source-tracking biomarker. Genomes classified in a novel viral lineage represented by isolate S-EIVl contained psbA, which is unprecedented for this lineage. Collectively, our findings indicated that the acquisition of photosynthesis AMGs is a widespread strategy used by cyanophages in aquatic ecosystems, and further indicated the existence of viral provinces in which certain viral species and/or genotypes are locally abundant.
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Affiliation(s)
- Carlos A Ruiz-Perez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, USA
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13
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Jo WK, Peters M, Kydyrmanov A, van de Bildt MWG, Kuiken T, Osterhaus A, Ludlow M. The Canine Morbillivirus Strain Associated with An Epizootic in Caspian Seals Provides New Insights into the Evolutionary History of this Virus. Viruses 2019; 11:E894. [PMID: 31557833 PMCID: PMC6832514 DOI: 10.3390/v11100894] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 08/07/2019] [Revised: 09/13/2019] [Accepted: 09/24/2019] [Indexed: 01/28/2023] Open
Abstract
Canine morbillivirus (canine distemper virus; CDV) is a worldwide distributed morbillivirus that causes sporadic cases and recurrent epizootics among an increasing number of wild, feral, and domestic animal species. We investigated the evolutionary history of CDV strains involved in the 1988 Lake Baikal (CDVPS88) and the 2000 Caspian Sea (CDVPC00) seal die-offs by recovery of full-length sequences from archived material using next-generation sequencing. Bayesian phylogenetic analyses indicated that CDVPC00 constitutes a novel strain in a separate clade (tentatively termed "Caspian") from the America-1 clade, which is comprised of older vaccine strains. The America-1/Caspian monophyletic group is positioned most basally with respect to other clades and is estimated to have separated from other CDV clades around 1832. Our results indicate that CDVPC00 recovered from the epizootic in the Caspian Sea in 2000 belongs to a previously undetected novel clade and constitutes the most ancestral wild-type CDV clade.
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Affiliation(s)
- Wendy K Jo
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany.
| | - Martin Peters
- Chemisches und Veterinäruntersuchungsamt Westfalen, 59821 Arnsberg, Germany.
| | - Aidyn Kydyrmanov
- Laboratory of Viral Ecology, Institute of Microbiology and Virology, 050010 Almaty, Kazakhstan.
| | | | - Thijs Kuiken
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands.
| | - Albert Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany.
| | - Martin Ludlow
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany.
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14
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Bai M, Cheng YH, Sun XQ, Wang ZY, Wang YX, Cui XL, Xiao W. Nine Novel Phages from a Plateau Lake in Southwest China: Insights into Aeromonas Phage Diversity. Viruses 2019; 11:v11070615. [PMID: 31284428 PMCID: PMC6669705 DOI: 10.3390/v11070615] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 04/28/2019] [Revised: 06/18/2019] [Accepted: 07/02/2019] [Indexed: 11/16/2022] Open
Abstract
Aeromonas species are common pathogens of fish and some of them can opportunistically cause infectious diseases in humans. The overuse of antibiotics has led to the emergence of bacterial drug-resistance. To date, only 51 complete genome sequences of Aeromonas phages are available in GenBank. Here, we report the isolation of nine Aeromonas phages from a plateau lake in China. The protein cluster, dot plot and ANI analyses were performed on all 60 currently sequenced Aeromonas phage genomes and classified into nine clusters and thirteen singletons. Among the nine isolated phages, the DNA-packaging strategy of cluster 2L372D (including 2L372D, 2L372X, 4L372D, 4L372XY) is unknown, while the other five phages use the headful (P22/Sf6) DNA-packaging strategy. Notably, the isolated phages with larger genomes conservatively encode auxiliary metabolism genes, DNA replication and metabolism genes, while in smaller phage genomes, recombination-related genes were conserved. Finally, we propose a new classification scheme for Aeromonas phages.
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Affiliation(s)
- Meng Bai
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China
| | - Ya-Hui Cheng
- Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming 650201, China
| | - Xue-Qin Sun
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China
| | - Zi-Yi Wang
- Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming 650201, China
| | - Yong-Xia Wang
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China
| | - Xiao-Long Cui
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China.
| | - Wei Xiao
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China.
- Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming 650500, China.
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15
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Getchell RG, First EJ, Bogdanowicz SM, Andrés JA, Schulman AT, Kramer J, Eckerlin GE, Farrell JM, Marquis H. Investigation of round goby viral haemorrhagic septicaemia outbreak in New York. J Fish Dis 2019; 42:1023-1033. [PMID: 31025373 DOI: 10.1111/jfd.13003] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
Eleven viral haemorrhagic septicaemia virus (VHSV) genotype IVb isolates were sequenced, and their genetic variation explored to determine the source of a VHS outbreak on the eastern shore of Cayuga Lake. An active fish kill of round gobies (Neogobius melanostomus, Pallas) was intensively sampled at King Ferry, NY and nearby Long Point State Park in May 2017. Gross lesions observed on 67 moribund round gobies and two rock bass (Ambloplites rupestris, Rafinesque) included moderately haemorrhagic internal organs and erythematous areas on the head, flank, and fins. RT-qPCR tests for VHSV were positive for all 69 fish. Viral isolation on epithelioma papulosum cyprinid cells showed cytopathic effect characteristic of VHSV for six round goby samples from King Ferry. The complete nucleotide sequence of the VHSV IVb genomes of five Cayuga Lake round goby isolates were derived on an Illumina platform along with 2017 VHSV IVb isolates from round gobies collected from the following: Lake Erie near Dunkirk, NY; the St. Lawrence River near Clayton and Cape Vincent, NY; and Lake St. Lawrence near Massena, NY. The phylogenetic tree created from these aligned sequences and four other complete VHSV IVb genomes shows Cayuga Lake isolates are closely related to the Lake Erie isolates.
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Affiliation(s)
- Rodman G Getchell
- Aquatic Animal Health Program, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Erika J First
- Aquatic Animal Health Program, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Steven M Bogdanowicz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Jose A Andrés
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Adam T Schulman
- Aquatic Animal Health Program, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Jordan Kramer
- Aquatic Animal Health Program, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Geofrey E Eckerlin
- Rome Field Station, New York State Department of Environmental Conservation, Rome, New York
| | - John M Farrell
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, New York
| | - Hélène Marquis
- Aquatic Animal Health Program, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York
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16
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Yin J, Wang Q, Wang Y, Li Y, Zeng W, Wu J, Ren Y, Tang Y, Gao C, Hu H, Bergmann SM. Development of a simple and rapid reverse transcription-loopmediated isothermal amplification (RT-LAMP) assay for sensitive detection of tilapia lake virus. J Fish Dis 2019; 42:817-824. [PMID: 30920677 DOI: 10.1111/jfd.12983] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 05/23/2023]
Abstract
Recently, substantial mortality of farmed and wild tilapia caused by tilapia lake virus (TiLV) infection has been observed worldwide. However, sensitive and reliable diagnostic method is limited. A reverse transcription-loopmediated isothermal amplification (RT-LAMP) assay has been applied for the detection of TiLV nucleotide sequence. Six primers targeting two locations on the target gene based on a highly conserved sequence in the segment 1 (S1) region of the TiLV genome have been designed. The optimized RT-LAMP reaction was maintained at the isothermal condition of 63°C for 45 min. And the amplifications could be verified by turbidity or a colour change with the addition of SYBR Green I. Subsequently, RT-LAMP products could be observed by a ladder pattern following gel electrophoresis. The species-specific assay showed that the method was sensitive enough to detect as low as 1.6 copies of viral particle, and the assay was highly specific because no cross-reactivity was observed with other pathogens, and had a diagnostic sensitivity and specificity of 100% when TiLV-positive samples and non-target virus were tested. In summary, all the results demonstrate that this RT-LAMP is a rapid, effective and sensitive method for TiLV detection in tilapia aquaculture.
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Affiliation(s)
- Jiyuan Yin
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Qing Wang
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yingying Wang
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yingying Li
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Weiwei Zeng
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jiexing Wu
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yan Ren
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yafang Tang
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, China
| | - Caixia Gao
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- College of Fisheries, Tianjin Agriculture University, Tianjin, China
| | - Huzi Hu
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- College of Fisheries, Tianjin Agriculture University, Tianjin, China
| | - Sven M Bergmann
- Institute of Infectology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
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17
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Numberger D, Dreier C, Vullioud C, Gabriel G, Greenwood AD, Grossart HP. Recovery of influenza A viruses from lake water and sediments by experimental inoculation. PLoS One 2019; 14:e0216880. [PMID: 31091283 PMCID: PMC6519785 DOI: 10.1371/journal.pone.0216880] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/30/2019] [Indexed: 11/19/2022] Open
Abstract
Influenza A viruses (IAV) are zoonotic pathogens relevant to human, domestic animal and wildlife health. Many avian IAVs are transmitted among waterfowl via a faecal-oral-route. Therefore, environmental water where waterfowl congregate may play an important role in the ecology and epidemiology of avian IAV. Water and sediment may sustain and transmit virus among individuals or species. It is unclear at what concentrations waterborne viruses are infectious or remain detectable. To address this, we performed lake water and sediment dilution experiments with varying concentrations or infectious doses of four IAV strains from seal, turkey, duck and gull. To test for infectivity of the IAV strains in a concentration dependent manner, we applied cultivation to specific pathogen free (SPF) embryonated chicken eggs and Madin-Darby Canine Kidney (MDCK) cells. IAV recovery was more effective from embryonated chicken eggs than MDCK cells for freshwater lake dilutions, whereas, MDCK cells were more effective for viral recovery from sediment samples. Low infectious dose (1 PFU/200 μL) was sufficient in most cases to detect and recover IAV from lake water dilutions. Sediment required higher initial infectious doses (≥ 100 PFU/200 μL).
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Affiliation(s)
| | - Carola Dreier
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Colin Vullioud
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Gülsah Gabriel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Alex D. Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- * E-mail: (HPG); (ADG)
| | - Hans-Peter Grossart
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany
- Freie Universität Berlin, Department of Veterinary Medicine, Institute for Virology, Berlin, Germany
- * E-mail: (HPG); (ADG)
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18
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Akhwale JK, Rohde M, Rohde C, Bunk B, Spröer C, Klenk HP, Boga HI, Wittmann J. Comparative genomic analysis of eight novel haloalkaliphilic bacteriophages from Lake Elmenteita, Kenya. PLoS One 2019; 14:e0212102. [PMID: 30763364 PMCID: PMC6375668 DOI: 10.1371/journal.pone.0212102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/28/2019] [Indexed: 12/17/2022] Open
Abstract
We report complete genome sequences of eight bacteriophages isolated from Haloalkaline Lake Elmenteita found on the floor of Kenyan Rift Valley. The bacteriophages were sequenced, annotated and a comparative genomic analysis using various Bioinformatics tools carried out to determine relatedness of the bacteriophages to each other, and to those in public databases. Basic genome properties like genome size, percentage coding density, number of open reading frames, percentage GC content and gene organizations revealed the bacteriophages had no relationship to each other. Comparison to other nucleotide sequences in GenBank database showed no significant similarities hence novel. At the amino acid level, phages of our study revealed mosaicism to genes with conserved domains to already described phages. Phylogenetic analyses of large terminase gene responsible for DNA packaging and DNA polymerase gene for replication further showed diversity among the bacteriophages. Our results give insight into diversity of bacteriophages in Lake Elmenteita and provide information on their evolution. By providing primary sequence information, this study not only provides novel sequences for biotechnological exploitation, but also sets stage for future studies aimed at better understanding of virus diversity and genomes from haloalkaline lakes in the Rift Valley.
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Affiliation(s)
- Juliah Khayeli Akhwale
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
- Department of Zoology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Manfred Rohde
- Helmholtz Centre for Infection Research, Central Facility for Microscopy, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Christine Rohde
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Johannes Wittmann
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
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19
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Cooksey EM, Singh G, Scott LC, Aw TG. Detection of coliphages and human adenoviruses in a subtropical estuarine lake. Sci Total Environ 2019; 649:1514-1521. [PMID: 30308919 DOI: 10.1016/j.scitotenv.2018.08.322] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 06/08/2023]
Abstract
Fecal indicator bacteria (FIB) have been used to assess fecal contamination in recreational water. However, enteric viruses have been shown to be more persistent in the environment and resistant to wastewater treatment than bacteria. Recently, U.S Environmental Protection Agency has proposed the use of coliphages as viral indicators to better protect against viral waterborne outbreaks. This study aimed to detect and determine correlation between coliphages (F-specific and somatic), fecal indicator bacteria (enterococci and fecal coliforms), and human enteric viruses (human adenovirus) in a subtropical brackish estuarine lake. Water samples were collected from 9 estuarine recreation sites on Lake Pontchartrain in southeast Louisiana. Water samples (n = 222, collected weekly) were analyzed for coliphages and fecal indicator bacteria using culture-based methods and large volume water samples (n = 54, collected monthly) were analyzed for human adenovirus using quantitative PCR. Somatic coliphage and F-specific coliphage were found in 93.7 and 65.2% of samples with geometric mean concentrations of 30 and 3 plaque forming units (PFU) per 100 mL, respectively. Enterococci, fecal coliforms, and adenovirus were found in all samples with geometric mean concentrations of 27 most probable number (MPN), 77 MPN, and 3.0 × 104 gene copies per 100 mL, respectively. Watersheds in suburban areas exhibited significantly higher concentrations of coliphages and fecal indicator bacteria, indicating potential fecal contamination from septic systems. There was no significant correlation (p > 0.05) observed between the presence of adenoviruses and fecal indicator bacteria and coliphages. The presence of human adenovirus in Lake Pontchartrain poses a significant public health problem for both recreational use and seafood harvesting as it increases exposure risks. This study demonstrated the lack of relationship between fecal indicators and human viral pathogen in Lake Pontchartrain supporting an alternative microbial surveillance system such as direct pathogen detection.
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Affiliation(s)
- Emily M Cooksey
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, United States of America
| | - Gulshan Singh
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, United States of America
| | - Laura C Scott
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, United States of America
| | - Tiong Gim Aw
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, United States of America.
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20
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Yang YF, Lu TH, Lin HC, Chen CY, Liao CM. Assessing the population transmission dynamics of tilapia lake virus in farmed tilapia. J Fish Dis 2018; 41:1439-1448. [PMID: 30003543 DOI: 10.1111/jfd.12845] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
A novel virus, tilapia lake virus (TiLV), has been identified as a key pathogen responsible for disease outbreak and mass mortality of farmed tilapia. We used a deterministic susceptible-infectious-mortality (SIM) model to derive key disease information appraised with published TiLV-induced cumulative mortality data. The relationship between tilapia mortality and TiLV exposure dosages was described by the Hill model. Furthermore, a disease control model was proposed to determine the status of controlled TiLV infection using a parsimonious control reproduction number (RC )-control line criterion. Results showed that the key disease determinants of transmission rate and basic reproduction number (R0 ) could be derived. The median R0 estimate was 2.59 in a cohabitation setting with 2.6 × 105 TCID50 fish-1 TiLV. The present RC -control model can be employed to determine whether TiLV containment is feasible in an outbreak farm by quantifying the current level of transmission. The SIM model can then be applied to predict what additional control is required to manage RC < 1. We offer valuable tools for aquaculture engineers and public health scientists the mechanistic-based assessment that allows a more rigorous evaluation of different control strategies to reduce waterborne diseases in aquaculture farming systems.
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Affiliation(s)
- Ying-Fei Yang
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan, ROC
| | - Tien-Hsuan Lu
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan, ROC
| | - Hsing-Chieh Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan, ROC
| | - Chi-Yun Chen
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan, ROC
| | - Chung-Min Liao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan, ROC
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21
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Wanjugi P, Sivaganesan M, Korajkic A, McMinn B, Kelty CA, Rhodes E, Cyterski M, Zepp R, Oshima K, Stachler E, Kinzelman J, Kurdas SR, Citriglia M, Hsu FC, Acrey B, Shanks OC. Incidence of somatic and F+ coliphage in Great Lake Basin recreational waters. Water Res 2018; 140:200-210. [PMID: 29715644 PMCID: PMC7366341 DOI: 10.1016/j.watres.2018.04.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 05/16/2023]
Abstract
There is a growing interest for the use of coliphage as an alternative indicator to assess fecal pollution in recreational waters. Coliphage are a group of viruses that infect Escherichia coli and are considered as potential surrogates to infer the likely presence of enteric viral pathogens. We report the use of a dead-end hollow fiber ultrafiltration single agar layer method to enumerate F+ and somatic coliphage from surface waters collected from three Great Lake areas. At each location, three sites (two beaches; one river) were sampled five days a week over the 2015 beach season (n = 609 total samples). In addition, culturable E. coli and enterococci concentrations, as well as 16 water quality and recreational area parameters were assessed such as rainfall, turbidity, dissolved oxygen, pH, and ultra violet absorbance. Overall, somatic coliphage levels ranged from non-detectable to 4.39 log10 plaque forming units per liter and were consistently higher compared to F+ (non-detectable to 3.15 log10 PFU/L), regardless of sampling site. Coliphage concentrations weakly correlated with cultivated fecal indicator bacteria levels (E. coli and enterococci) at 75% of beach sites tested in study (r = 0.28 to 0.40). In addition, ultraviolet light absorption and water temperature were closely associated with coliphage concentrations, but not fecal indicator bacteria levels suggesting different persistence trends in Great Lake waters between indicator types (bacteria versus virus). Finally, implications for coliphage water quality management and future research directions are discussed.
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Affiliation(s)
- Pauline Wanjugi
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Asja Korajkic
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Brian McMinn
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Catherine A Kelty
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Eric Rhodes
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Mike Cyterski
- United States Environmental Protection Agency, Ecosystems Assessment Branch, National Exposure Research Laboratory, Athens, GA 30605, USA
| | - Richard Zepp
- United States Environmental Protection Agency, Ecosystems Assessment Branch, National Exposure Research Laboratory, Athens, GA 30605, USA
| | - Kevin Oshima
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Elyse Stachler
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | | | | | - Mark Citriglia
- Northeast Ohio Regional Sewer District, Cuyahoga Heights, OH 44115, USA
| | - Fu-Chih Hsu
- Scientific Methods Inc, Granger, IN 46530, USA
| | - Brad Acrey
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA.
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22
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McMinn BR, Rhodes ER, Huff EM, Wanjugi P, Ware MM, Nappier SP, Cyterski M, Shanks OC, Oshima K, Korajkic A. Comparison of somatic and F+ coliphage enumeration methods with large volume surface water samples. J Virol Methods 2018; 261:63-66. [PMID: 30096350 PMCID: PMC7082814 DOI: 10.1016/j.jviromet.2018.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/02/2018] [Accepted: 08/06/2018] [Indexed: 12/21/2022]
Abstract
Coliphages are alternative fecal indicators that may be suitable surrogates for viral pathogens, but majority of standard detection methods utilize insufficient volumes for routine detection in environmental waters. We compared three somatic and F+ coliphage methods based on a paired measurement from 1 L samples collected from the Great Lakes (n = 74). Methods include: 1) dead-end hollow fiber ultrafilter with single agar layer (D-HFUF-SAL); 2) modified SAL (M-SAL); and 3) direct membrane filtration (DMF) technique. Overall, D-HFUF-SAL outperformed other methods as it yielded the lowest frequency of non-detects [(ND); 10.8%] and the highest average concentrations of recovered coliphage for positive samples (2.51 ± 1.02 [standard deviation, SD] log10 plaque forming unit/liter (PFU/L) and 0.79 ± 0.71 (SD) log10 PFU/L for somatic and F+, respectively). M-SAL yielded 29.7% ND and average concentrations of 2.26 ± 1.15 (SD) log10 PFU/L (somatic) and 0.59 ± 0.82 (SD) log10 PFU/L (F+ ). DMF performance was inferior to D-HFUF-SAL and M-SAL methods (ND of 65.6%; average somatic coliphage concentration 1.52 ± 1.32 [SD] log10 PFU/L, no F+ detected), indicating this procedure is unsuitable for 1 L surface water sample volumes. This study represents an important step toward the use of a coliphage method for recreational water quality criteria purposes.
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Affiliation(s)
- Brian R McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Eric R Rhodes
- United States Environmental Protection Agency, Office of Research and Development, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Emma M Huff
- United States Environmental Protection Agency, Office of Research and Development, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Pauline Wanjugi
- United States Environmental Protection Agency, Office of Research and Development, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Michael M Ware
- United States Environmental Protection Agency, Office of Research and Development, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Sharon P Nappier
- Office of Water, 1200 Pennsylvania Avenue NW, Washington, D.C. 20460, United States
| | - Mike Cyterski
- Office of Research and Development, 960 College Station Rd., Athens, GA 30605, United States
| | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Kevin Oshima
- United States Environmental Protection Agency, Office of Research and Development, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States.
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23
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Graciaa DS, Cope JR, Roberts VA, Cikesh BL, Kahler AM, Vigar M, Hilborn ED, Wade TJ, Backer LC, Montgomery SP, Secor WE, Hill VR, Beach MJ, Fullerton KE, Yoder JS, Hlavsa MC. Outbreaks Associated with Untreated Recreational Water - United States, 2000-2014. MMWR Morb Mortal Wkly Rep 2018; 67:701-706. [PMID: 29953425 PMCID: PMC6023190 DOI: 10.15585/mmwr.mm6725a1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Outbreaks associated with untreated recreational water can be caused by pathogens, toxins, or chemicals in fresh water (e.g., lakes, rivers) or marine water (e.g., ocean). During 2000-2014, public health officials from 35 states and Guam voluntarily reported 140 untreated recreational water-associated outbreaks to CDC. These outbreaks resulted in at least 4,958 cases of disease and two deaths. Among the 95 outbreaks with a confirmed infectious etiology, enteric pathogens caused 80 (84%); 21 (22%) were caused by norovirus, 19 (20%) by Escherichia coli, 14 (15%) by Shigella, and 12 (13%) by Cryptosporidium. Investigations of these 95 outbreaks identified 3,125 cases; 2,704 (87%) were caused by enteric pathogens, including 1,459 (47%) by norovirus, 362 (12%) by Shigella, 314 (10%) by Cryptosporidium, and 155 (5%) by E. coli. Avian schistosomes were identified as the cause in 345 (11%) of the 3,125 cases. The two deaths were in persons affected by a single outbreak (two cases) caused by Naegleria fowleri. Public parks (50 [36%]) and beaches (45 [32%]) were the leading settings associated with the 140 outbreaks. Overall, the majority of outbreaks started during June-August (113 [81%]); 65 (58%) started in July. Swimmers and parents of young swimmers can take steps to minimize the risk for exposure to pathogens, toxins, and chemicals in untreated recreational water by heeding posted advisories closing the beach to swimming; not swimming in discolored, smelly, foamy, or scummy water; not swimming while sick with diarrhea; and limiting water entering the nose when swimming in warm freshwater.
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24
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Hewson I, Bistolas KSI, Button JB, Jackson EW. Occurrence and seasonal dynamics of RNA viral genotypes in three contrasting temperate lakes. PLoS One 2018; 13:e0194419. [PMID: 29543885 PMCID: PMC5854377 DOI: 10.1371/journal.pone.0194419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/04/2018] [Indexed: 11/18/2022] Open
Abstract
Decades of research have demonstrated the crucial importance of viruses in freshwater ecosystems. However, few studies have focused on the seasonal dynamics and potential hosts of RNA viruses. We surveyed microbial-sized (i.e. 5-0.2 μm) mixed community plankton transcriptomes for RNA viral genomes and investigated their distribution between microbial and macrobial plankton over a seasonal cycle across three temperate lakes by quantitative reverse transcriptase PCR (qRT-PCR). A total of 30 contigs bearing similarity to RNA viral genomes were recovered from a global assembly of 30 plankton RNA libraries. Of these, only 13 were found in >2 libraries and recruited >100 reads (of 9.13 x 107 total reads), representing several picornaviruses, two tobamoviruses and a reovirus. We quantified the abundance of four picornaviruses and the reovirus monthly from August 2014 to May 2015. Patterns of viral abundance in the >5 μm size fraction and representation in microbial-sized community RNA libraries over time suggest that one picornavirus genotype (TS24835) and the reovirus (TS148892) may infect small (<5 μm) eukaryotic microorganisms, while two other picornaviruses (TS24641 and TS4340) may infect larger (>5 μm) eukaryotic microorganisms or metazoa. Our data also suggest that picornavirus TS152062 may originate from an allochthonous host. All five viral genotypes were present in at least one size fraction across all 3 lakes during the year, suggesting that RNA viruses may easily disperse between adjacent aquatic habitats. Our data therefore demonstrate that RNA viruses are widespread in temperate lacustrine ecosystems, and may provide evidence of viral infection in larger eukaryotes (including metazoa) inhabiting the lakes.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Kalia S. I. Bistolas
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Jason B. Button
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
| | - Elliot W. Jackson
- Department of Microbiology, Cornell University, Ithaca, NY United States of America
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25
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Surachetpong W, Janetanakit T, Nonthabenjawan N, Tattiyapong P, Sirikanchana K, Amonsin A. Outbreaks of Tilapia Lake Virus Infection, Thailand, 2015-2016. Emerg Infect Dis 2018; 23:1031-1033. [PMID: 28518020 PMCID: PMC5443430 DOI: 10.3201/eid2306.161278] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
During 2015–2016, several outbreaks of tilapia lake virus infection occurred among tilapia in Thailand. Phylogenetic analysis showed that the virus from Thailand grouped with a tilapia virus (family Orthomyxoviridae) from Israel. This emerging virus is a threat to tilapia aquaculture in Asia and worldwide.
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26
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Cabello-Yeves PJ, Zemskaya TI, Rosselli R, Coutinho FH, Zakharenko AS, Blinov VV, Rodriguez-Valera F. Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal. Appl Environ Microbiol 2018; 84:e02132-17. [PMID: 29079621 PMCID: PMC5734018 DOI: 10.1128/aem.02132-17] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [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: 09/27/2017] [Accepted: 10/19/2017] [Indexed: 11/20/2022] Open
Abstract
We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from the water column under the ice cover (5 and 20 m deep) in March 2016 have been deep sequenced and the reads assembled to generate metagenome-assembled genomes (MAGs) that are representative of the microbes living in this special environment. Compared with freshwater bodies studied around the world, Lake Baikal had an unusually high fraction of Verrucomicrobia Other groups, such as Actinobacteria and Proteobacteria, were in proportions similar to those found in other lakes. The genomes (and probably cells) tended to be small, presumably reflecting the extremely oligotrophic and cold prevalent conditions. Baikal microbes are novel lineages recruiting very little from other water bodies and are distantly related to other freshwater microbes. Despite their novelty, they showed the closest relationship to genomes discovered by similar approaches from other freshwater lakes and reservoirs. Some of them were particularly similar to MAGs from the Baltic Sea, which, although it is brackish, connected to the ocean, and much more eutrophic, has similar climatological conditions. Many of the microbes contained rhodopsin genes, indicating that, in spite of the decreased light penetration allowed by the thick ice/snow cover, photoheterotrophy could be widespread in the water column, either because enough light penetrates or because the microbes are already adapted to the summer ice-less conditions. We have found a freshwater SAR11 subtype I/II representative showing striking synteny with Pelagibacterubique strains, as well as a phage infecting the widespread freshwater bacterium PolynucleobacterIMPORTANCE Despite the increasing number of metagenomic studies on different freshwater bodies, there is still a missing component in oligotrophic cold lakes suffering from long seasonal frozen cycles. Here, we describe microbial genomes from metagenomic assemblies that appear in the upper water column of Lake Baikal, the largest and deepest freshwater body on Earth. This lake is frozen from January to May, which generates conditions that include an inverted temperature gradient (colder up), decrease in light penetration due to ice, and, especially, snow cover, and oligotrophic conditions more similar to the open-ocean and high-altitude lakes than to other freshwater or brackish systems. As could be expected, most reconstructed genomes are novel lineages distantly related to others in cold environments, like the Baltic Sea and other freshwater lakes. Among them, there was a broad set of streamlined microbes with small genomes/intergenic spacers, including a new nonmarine Pelagibacter-like (subtype I/II) genome.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Tamara I Zemskaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Riccardo Rosselli
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Felipe H Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Alexandra S Zakharenko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Vadim V Blinov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
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Throckmorton E, Brenden T, Peters AK, Newcomb TJ, Whelan GE, Faisal M. Potential Reservoirs and Risk Factors for VHSV IVb in an Enzootic System: Budd Lake, Michigan. J Aquat Anim Health 2017; 29:31-42. [PMID: 28166454 DOI: 10.1080/08997659.2016.1254121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Viral hemorrhagic septicemia virus genotype IVb (VHSV IVb) has caused major, sporadic fish die-offs in the Laurentian Great Lakes region of North America since 2005. Presently, factors affecting VHSV IVb persistence in enzootic systems are not well understood. Even with annual surveillance, the virus can go undetected for several years after an outbreak before again re-emerging, which suggests that the virus is maintained in the system either below detectable levels or in untested reservoirs. The aim of this study was to identify potential reservoirs of VHSV IVb in Budd Lake, Michigan; VHSV IVb was first detected in Budd Lake in 2007 but remained undetected until 2011. Additionally, we explored the susceptibility of naive fish introduced into a water body enzootic for VHSV IVb by stocking age-0 Largemouth Bass Micropterus salmoides at varying densities into enclosures in the lake. The virus was not detected among samples of the fishes Notropis spp. and Lepomis spp., cylindrical papershell mussels Anodontoides ferussacianus, leeches (subclass Hirudinea), sediment, or water. However, the virus was successfully isolated from amphipods (family Hyalellidae) and Largemouth Bass held in the enclosures. Our finding of VHSV IVb in Hyalellidae amphipods in combination with other research that has detected the virus in Diporeia spp., a large benthic amphipod important as a food resource to Great Lake fishes, suggests that benthic macroinvertebrates are a reservoir for VHSV IVb in infected systems. If there are environmental reservoirs for VHSV IVb in infected systems, they are likely unevenly distributed. Findings of this study add to our understanding of the seemingly complex ecology of this deadly and economically detrimental virus. Received February 22, 2016; accepted October 16, 2016.
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Affiliation(s)
- Elizabeth Throckmorton
- a Department of Fisheries and Wildlife , Michigan State University , 480 Wilson Road, East Lansing , Michigan 48824 , USA
| | - Travis Brenden
- b Quantitative Fisheries Center, Department of Fisheries and Wildlife , Michigan State University , 293 Farm Lane, East Lansing , Michigan 48824 , USA
| | - Amber K Peters
- a Department of Fisheries and Wildlife , Michigan State University , 480 Wilson Road, East Lansing , Michigan 48824 , USA
| | - Tammy J Newcomb
- c Michigan Department of Natural Resources , Post Office Box 30028, 525 West Allegan Street, Lansing , Michigan 48933 , USA
| | - Gary E Whelan
- d Michigan Department of Natural Resources, Fisheries Division , Post Office Box 30446, Lansing , Michigan 48909 , USA
| | - Mohamed Faisal
- a Department of Fisheries and Wildlife , Michigan State University , 480 Wilson Road, East Lansing , Michigan 48824 , USA
- e Department of Pathobiology and Diagnostic Investigation , Michigan State University , 1129 Farm Lane, East Lansing , Michigan 48824 , USA
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28
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Colombet J, Robin A, Sime-Ngando T. Genotypic, size and morphological diversity of virioplankton in a deep oligomesotrophic freshwater lake (Lac Pavin, France). J Environ Sci (China) 2017; 53:48-59. [PMID: 28372760 DOI: 10.1016/j.jes.2016.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 06/07/2023]
Abstract
We examined changes in morphological and genomic diversities of viruses by means of transmission electronic microscopy and pulsed field gel electrophoresis (PFGE) over a nine-month period (April-December 2005) at four different depths in the oligomesotrophic Lac Pavin. We found that the majority of viruses in this lake belonged to the family of Siphoviridae or were untailed, with capsid sizes ranging from 30 to 60nm, and exhibited genome sizes ranging from 15 to 45kb. On average, 12 different genotypes dominated each of the PFGE fingerprints. The highest genomic viral richness was recorded in summer (mean=14 bands per PFGE fingerprint) and in the epilimnion (mean=13 bands per PFGE fingerprint). Among the physico-chemical and biological variables considered, the availability of the hosts appeared to be the main factor regulating the variations in the viral diversity.
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Affiliation(s)
- Jonathan Colombet
- Laboratory Microorganisms: Genome and Environment, Clermont University Blaise Pascal, UMR CNRS 6023, 24 avenue des Landais, BP 80026, F-63171 Aubière, France.
| | - Agnès Robin
- CIRAD, UMR Eco&Sols, 2 place Viala, 34060 Montpellier Cedex 1, France
| | - Télesphore Sime-Ngando
- Laboratory Microorganisms: Genome and Environment, Clermont University Blaise Pascal, UMR CNRS 6023, 24 avenue des Landais, BP 80026, F-63171 Aubière, France
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D'Ugo E, Marcheggiani S, Fioramonti I, Giuseppetti R, Spurio R, Helmi K, Guillebault D, Medlin LK, Simeonovski I, Boots B, Breitenbach U, Koker L, Albay M, Mancini L. Detection of Human Enteric Viruses in Freshwater from European Countries. Food Environ Virol 2016; 8:206-214. [PMID: 27117764 DOI: 10.1007/s12560-016-9238-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/18/2016] [Indexed: 06/05/2023]
Abstract
The transmission of water-borne pathogens typically occurs by a faecal-oral route, through inhalation of aerosols, or by direct or indirect contact with contaminated water. Previous molecular-based studies have identified viral particles of zoonotic and human nature in surface waters. Contaminated water can lead to human health issues, and the development of rapid methods for the detection of pathogenic microorganisms is a valuable tool for the prevention of their spread. The aims of this work were to determine the presence and identity of representative human pathogenic enteric viruses in water samples from six European countries by quantitative polymerase chain reaction (q-PCR) and to develop two quantitative PCR methods for Adenovirus 41 and Mammalian Orthoreoviruses. A 2-year survey showed that Norovirus, Mammalian Orthoreovirus and Adenoviruses were the most frequently identified enteric viruses in the sampled surface waters. Although it was not possible to establish viability and infectivity of the viruses considered, the detectable presence of pathogenic viruses may represent a potential risk for human health. The methodology developed may aid in rapid detection of these pathogens for monitoring quality of surface waters.
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Affiliation(s)
- Emilio D'Ugo
- Quality and Fishfarm Unit, Department Environmental Environment & Primary Prevention, Istituto Superiore di Sanità, Rome, Italy.
| | - Stefania Marcheggiani
- Quality and Fishfarm Unit, Department Environmental Environment & Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Ilaria Fioramonti
- Quality and Fishfarm Unit, Department Environmental Environment & Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Roberto Giuseppetti
- Quality and Fishfarm Unit, Department Environmental Environment & Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Roberto Spurio
- School of Biosciences and Veterinary Medicine, University of Camerino, Ascoli Piceno, Italy
| | - Karim Helmi
- Veolia Rechercheur & Innovation, Saint-Maurice, France
| | | | - Linda K Medlin
- Microbia Environnement, Observatoire Océanologique, 66650, Banyuls/Mer, France
| | - Ivan Simeonovski
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Bas Boots
- UCD School of Biosystems Engineering, Agriculture and Food Science Centre, Dublin, Ireland
| | | | - Latife Koker
- Fisheries Faculty, Istanbul University, Istanbul, Turkey
| | - Meric Albay
- Fisheries Faculty, Istanbul University, Istanbul, Turkey
| | - Laura Mancini
- Quality and Fishfarm Unit, Department Environmental Environment & Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
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Quispe CF, Sonderman O, Seng A, Rasmussen B, Weber G, Mueller C, Dunigan DD, Van Etten JL. Three-year survey of abundance, prevalence and genetic diversity of chlorovirus populations in a small urban lake. Arch Virol 2016; 161:1839-47. [PMID: 27068168 DOI: 10.1007/s00705-016-2853-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/30/2016] [Indexed: 11/28/2022]
Abstract
Inland water environments cover about 2.5 percent of our planet and harbor huge numbers of known and still unknown microorganisms. In this report, we examined water samples for the abundance, prevalence, and genetic diversity of a group of infectious viruses (chloroviruses) that infect symbiotic chlorella-like green algae. Samples were collected on a weekly basis for a period of 24 to 36 months from a recreational freshwater lake in Lincoln, Nebraska, and assayed for infectious viruses by plaque assay. The numbers of infectious virus particles were both host- and site-dependent. The consistent fluctuations in numbers of viruses suggest their impact as key factors in shaping microbial community structures in the water surface. Even in low-viral-abundance months, infectious chlorovirus populations were maintained, suggesting either that the viruses are very stable or that there is ongoing viral production in natural hosts.
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Affiliation(s)
- Cristian F Quispe
- Department of Plant Pathology, Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
- School of Biological Science, Manter Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
| | - Olivia Sonderman
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Anya Seng
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Brenna Rasmussen
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Garrett Weber
- Department of Plant Pathology, Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Claire Mueller
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - David D Dunigan
- Department of Plant Pathology, Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - James L Van Etten
- Department of Plant Pathology, Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
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Skvortsov T, de Leeuwe C, Quinn JP, McGrath JW, Allen CCR, McElarney Y, Watson C, Arkhipova K, Lavigne R, Kulakov LA. Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland. PLoS One 2016; 11:e0150361. [PMID: 26927795 PMCID: PMC4771703 DOI: 10.1371/journal.pone.0150361] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/12/2016] [Indexed: 11/18/2022] Open
Abstract
Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world’s major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column.
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Affiliation(s)
- Timofey Skvortsov
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Colin de Leeuwe
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - John P. Quinn
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - John W. McGrath
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Christopher C. R. Allen
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Yvonne McElarney
- Agri-Food & Biosciences Institute, Belfast, Northern Ireland, United Kingdom
| | - Catherine Watson
- Agri-Food & Biosciences Institute, Belfast, Northern Ireland, United Kingdom
| | - Ksenia Arkhipova
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Leonid A. Kulakov
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
- * E-mail:
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Elmahdy EM, Fongaro G, Schissi CD, Petrucio MM, Barardi CRM. Enteric viruses in surface water and sediment samples from the catchment area of Peri Lagoon, Santa Catarina State, Brazil. J Water Health 2016; 14:142-154. [PMID: 26837838 DOI: 10.2166/wh.2015.295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This paper aims to quantify human adenovirus (HAdV), rotavirus species A (RVA), and hepatitis A virus (HAV) in surface water and sediments and to determine the viability of HAdV in these samples. Water and sediment samples were collected, and HAdV, RVA, and HAV were quantified by real-time polymerase chain reaction (PCR); HAdV was also evaluated for infectivity by a plaque assay (PA). For the water samples, HAdV was detected in 70.8% of the summer collections, with 82.4% containing infectious HAdV; the HAdV incidence in winter was 62.5%. For the sediment samples, the incidence of HAdV was 37.5% in the summer collections, with 66.7% containing infectious HAdV; the HAdV incidence in winter was 37.5%. RVA was detected in 20.8 and 45.8% of surface water samples collected in summer and winter, respectively, and 8.3 and 12.5% of sediment samples collected in summer and winter, respectively. HAV was detected only in surface waters, with 54.8 and 12.5% positivity in summer and winter samples, respectively. This study demonstrated that enteric viruses are present in water and sediments and that the presence of infectious viruses should be investigated whenever possible for quantitative microbial risk assessment studies. Combined analyses of water and sediments are important for reliable public health risk analysis of recreational and lagoon waters.
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Affiliation(s)
- E M Elmahdy
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Campus Universitário s/n, Trindade, Florianópolis, SC, CEP. 88040-900, Brazil E-mail:
| | - G Fongaro
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Campus Universitário s/n, Trindade, Florianópolis, SC, CEP. 88040-900, Brazil E-mail:
| | - C D Schissi
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Campus Universitário s/n, Trindade, Florianópolis, SC, CEP. 88040-900, Brazil E-mail:
| | - M M Petrucio
- Laboratório de Ecologia de Águas Continentais, Departamento de Ecologia e Zoologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Campus Universitário s/n, Trindade, Florianópolis, SC, CEP. 88040-970, Brazil
| | - C R M Barardi
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Campus Universitário s/n, Trindade, Florianópolis, SC, CEP. 88040-900, Brazil E-mail:
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Corsi SR, Borchardt MA, Carvin RB, Burch TR, Spencer SK, Lutz MA, McDermott CM, Busse KM, Kleinheinz GT, Feng X, Zhu J. Human and Bovine Viruses and Bacteria at Three Great Lakes Beaches: Environmental Variable Associations and Health Risk. Environ Sci Technol 2016; 50:987-95. [PMID: 26720156 DOI: 10.1021/acs.est.5b04372] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Waterborne pathogens were measured at three beaches in Lake Michigan, environmental factors for predicting pathogen concentrations were identified, and the risk of swimmer infection and illness was estimated. Waterborne pathogens were detected in 96% of samples collected at three Lake Michigan beaches in summer, 2010. Samples were quantified for 22 pathogens in four microbial categories (human viruses, bovine viruses, protozoa, and pathogenic bacteria). All beaches had detections of human and bovine viruses and pathogenic bacteria indicating influence of multiple contamination sources at these beaches. Occurrence ranged from 40 to 87% for human viruses, 65-87% for pathogenic bacteria, and 13-35% for bovine viruses. Enterovirus, adenovirus A, Salmonella spp., Campylobacter jejuni, bovine polyomavirus, and bovine rotavirus A were present most frequently. Variables selected in multiple regression models used to explore environmental factors that influence pathogens included wave direction, cloud cover, currents, and water temperature. Quantitative Microbial Risk Assessment was done for C. jejuni, Salmonella spp., and enteroviruses to estimate risk of infection and illness. Median infection risks for one-time swimming events were approximately 2 × 10(-5), 8 × 10(-6), and 3 × 10(-7) [corrected] for C. jejuni, Salmonella spp., and enteroviruses, respectively. Results highlight the importance of investigating multiple pathogens within multiple categories to avoid underestimating the prevalence and risk of waterborne pathogens.
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Affiliation(s)
- Steven R Corsi
- U.S. Geological Survey, Wisconsin Water Science Center , 8505 Research Way, Middleton, Wisconsin 53562, United States
| | - Mark A Borchardt
- U.S. Department of Agriculture, Agricultural Research Service , 2615 Yellowstone Dr., Marshfield, Wisconsin 54449, United States
| | - Rebecca B Carvin
- U.S. Geological Survey, Wisconsin Water Science Center , 8505 Research Way, Middleton, Wisconsin 53562, United States
| | - Tucker R Burch
- U.S. Geological Survey, Wisconsin Water Science Center , 2615 Yellowstone Drive, Marshfield, Wisconsin 54449, United States
| | - Susan K Spencer
- U.S. Department of Agriculture, Agricultural Research Service , 2615 Yellowstone Dr., Marshfield, Wisconsin 54449, United States
| | - Michelle A Lutz
- U.S. Geological Survey, Wisconsin Water Science Center , 8505 Research Way, Middleton, Wisconsin 53562, United States
| | - Colleen M McDermott
- Department of Biology and Microbiology, University of Wisconsin Oshkosh , 800 Algoma Boulevard, Oshkosh, Wisconsin 54901, United States
| | - Kimberly M Busse
- Department of Biology and Microbiology, University of Wisconsin Oshkosh , 800 Algoma Boulevard, Oshkosh, Wisconsin 54901, United States
| | - Gregory T Kleinheinz
- Department of Biology and Microbiology, University of Wisconsin Oshkosh , 800 Algoma Boulevard, Oshkosh, Wisconsin 54901, United States
| | - Xiaoping Feng
- Department of Statistics, University of Wisconsin-Madison , 1300 University Avenue, Madison, Wisconsin 53706, United States
| | - Jun Zhu
- Department of Statistics, University of Wisconsin-Madison , 1300 University Avenue, Madison, Wisconsin 53706, United States
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Maurer CP, Simonetti AB, Staggemeier R, Rigotto C, Heinzelmann LS, Spilki FR. Adenovirus, enterovirus and thermotolerant coliforms in recreational waters from Lake Guaíba beaches, Porto Alegre, Brazil. J Water Health 2015; 13:1123-1129. [PMID: 26608773 DOI: 10.2166/wh.2015.277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In the present study, molecular detection of human adenoviruses (HAdV) and enteroviruses (EV) was performed in surface water samples collected from beaches Ipanema and Lami, located on the shores of Lake Guaíba, city of Porto Alegre, RS, southern Brazil. Furthermore, water safety was evaluated by counting thermotolerant coliforms (TC), following local government regulations. A total of 36 samples were collected monthly from six different sites along the beaches. Viral genomes were found in 30 (83.3%) samples. The higher detection rate was observed for HAdV (77.8%), followed by EV (22.2%). Although low concentrations of TC have been found, the occurrence of viral genomes in water samples was frequent and may pose a potential risk of infection for people bathing in these beaches.
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Affiliation(s)
- C P Maurer
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul-UFRGS, Av. Sarmento Leite, 500, CEP 90050-170, Porto Alegre, Rio Grande do Sul, Brazil
| | - A B Simonetti
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul-UFRGS, Av. Sarmento Leite, 500, CEP 90050-170, Porto Alegre, Rio Grande do Sul, Brazil
| | - R Staggemeier
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, Rio Grande do Sul, Brazil and Programa de Pós-Graduação em Qualidade Ambiental, Universidade Feevale, CEP 93352-000, Novo Hamburgo, Rio Grande do Sul, Brazil E-mail:
| | - C Rigotto
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, Rio Grande do Sul, Brazil and Programa de Pós-Graduação em Qualidade Ambiental, Universidade Feevale, CEP 93352-000, Novo Hamburgo, Rio Grande do Sul, Brazil E-mail:
| | - L S Heinzelmann
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, Rio Grande do Sul, Brazil and Programa de Pós-Graduação em Qualidade Ambiental, Universidade Feevale, CEP 93352-000, Novo Hamburgo, Rio Grande do Sul, Brazil E-mail:
| | - F R Spilki
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, Rio Grande do Sul, Brazil and Programa de Pós-Graduação em Qualidade Ambiental, Universidade Feevale, CEP 93352-000, Novo Hamburgo, Rio Grande do Sul, Brazil E-mail:
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Stepien CA, Pierce LR, Leaman DW, Niner MD, Shepherd BS. Gene Diversification of an Emerging Pathogen: A Decade of Mutation in a Novel Fish Viral Hemorrhagic Septicemia (VHS) Substrain since Its First Appearance in the Laurentian Great Lakes. PLoS One 2015; 10:e0135146. [PMID: 26313549 PMCID: PMC4552161 DOI: 10.1371/journal.pone.0135146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/18/2015] [Indexed: 12/30/2022] Open
Abstract
Viral Hemorrhagic Septicemia virus (VHSv) is an RNA rhabdovirus, which causes one of the world's most serious fish diseases, infecting >80 freshwater and marine species across the Northern Hemisphere. A new, novel, and especially virulent substrain—VHSv-IVb—first appeared in the Laurentian Great Lakes about a decade ago, resulting in massive fish kills. It rapidly spread and has genetically diversified. This study analyzes temporal and spatial mutational patterns of VHSv-IVb across the Great Lakes for the novel non-virion (Nv) gene that is unique to this group of novirhabdoviruses, in relation to its glycoprotein (G), phosphoprotein (P), and matrix (M) genes. Results show that the Nv-gene has been evolving the fastest (k = 2.0x10-3 substitutions/site/year), with the G-gene at ~1/7 that rate (k = 2.8x10-4). Most (all but one) of the 12 unique Nv- haplotypes identified encode different amino acids, totaling 26 changes. Among the 12 corresponding G-gene haplotypes, seven vary in amino acids with eight total changes. The P- and M- genes are more evolutionarily conserved, evolving at just ~1/15 (k = 1.2x10-4) of the Nv-gene’s rate. The 12 isolates contained four P-gene haplotypes with two amino acid changes, and six M-gene haplotypes with three amino acid differences. Patterns of evolutionary changes coincided among the genes for some of the isolates, but appeared independent in others. New viral variants were discovered following the large 2006 outbreak; such differentiation may have been in response to fish populations developing resistance, meriting further investigation. Two 2012 variants were isolated by us from central Lake Erie fish that lacked classic VHSv symptoms, having genetically distinctive Nv-, G-, and M-gene sequences (with one of them also differing in its P-gene); they differ from each other by a G-gene amino acid change and also differ from all other isolates by a shared Nv-gene amino acid change. Such rapid evolutionary differentiation may allow new viral variants to evade fish host recognition and immune responses, facilitating long-time persistence along with expansion to new geographic areas.
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Affiliation(s)
- Carol A. Stepien
- Great Lakes Genetics/Genomics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, Ohio, 43616, United States of America
- * E-mail:
| | - Lindsey R. Pierce
- Great Lakes Genetics/Genomics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, Ohio, 43616, United States of America
| | - Douglas W. Leaman
- Department of Biological Sciences, The University of Toledo, Toledo, Ohio, 43606, United States of America
| | - Megan D. Niner
- Great Lakes Genetics/Genomics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, Ohio, 43616, United States of America
| | - Brian S. Shepherd
- ARS/USDA/University of Wisconsin at Milwaukee/School of Freshwater Sciences, Milwaukee, Wisconsin, 53204, United States of America
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Abstract
Ballast water is one of the most important vectors for the transport of non-native species to new aquatic environments. Due to the development of new ballast water quality standards for viruses, this study aimed to determine the taxonomic diversity and composition of viral communities (viromes) in ballast and harbor waters using metagenomics approaches. Ballast waters from different sources within the North America Great Lakes and paired harbor waters were collected around the Port of Duluth-Superior. Bioinformatics analysis of over 550 million sequences showed that a majority of the viral sequences could not be assigned to any taxa associated with reference sequences, indicating the lack of knowledge on viruses in ballast and harbor waters. However, the assigned viruses were dominated by double-stranded DNA phages, and sequences associated with potentially emerging viral pathogens of fish and shrimp were detected with low amino acid similarity in both ballast and harbor waters. Annotation-independent comparisons showed that viromes were distinct among the Great Lakes, and the Great Lakes viromes were closely related to viromes of other cold natural freshwater systems but distant from viromes of marine and human designed/managed freshwater systems. These results represent the most detailed characterization to date of viruses in ballast water, demonstrating their diversity and the potential significance of the ship-mediated spread of viruses.
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Affiliation(s)
- Yiseul Kim
- †Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tiong Gim Aw
- ‡Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tracy K Teal
- †Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Joan B Rose
- †Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- ‡Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan 48824, United States
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Zlot A, Simckes M, Vines J, Reynolds L, Sullivan A, Scott MK, McLuckie JM, Kromer D, Hill VR, Yoder JS, Hlavsa MC. Norovirus Outbreak Associated With a Natural Lake Used for Recreation-Oregon, 2014. Am J Transplant 2015; 15:2001-5. [PMID: 26086301 DOI: 10.1111/ajt.13404] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Yao Y, Xu CL, Shi JH, Zhu Y, Li YF, Bai T, Li FC, Cai T, Yuan F, Chen T, Yang H, Li WC, Zhang HJ, Zhang H, Shu YL. Phylogenetic and Molecular Analysis of an H7N7 Avian Influenza Virus Isolated in East Dongting Lake in 2012. Biomed Environ Sci 2015; 28:518-526. [PMID: 26248736 DOI: 10.3967/bes2015.074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 06/10/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVE In March 2012, an H7N7 subtype avian influenza virus (AIV) named A/wild goose/Dongting/PC0360/2012 (H7N7) (DT/PC0360) was recovered from a wild goose in East Dongting Lake. We performed whole-genome sequencing of the isolate, and analyzed the phylogenetic and molecular characterization. METHODS RNA was extracted from environment samples (including fecal samples from wild bird or domestic ducks, and water samples) for detecting the presence of Influenza A Virus targeting Matrix gene, using realtime RT-PCR assay. The positive samples were performed virus isolation with embryonated eggs. The subtype of the isolates were identified by RT-PCR assay with the H1-H16 and N1-N9 primer set. The whole-genome sequencing of isolates were performed. Phylogenetic and molecular characterizations of the eight genes of the isolates were analyzed. RESULTS Our results suggested that all the eight gene segments of DT/PC0360 belonged to the Eurasian gene pool, and the HA gene were belonged to distinct sublineage with H7N9 AIV which caused outbreaks in Mainland China in 2013. The hemagglutinin cleavage site of HA of DT/PC0360 showed characterization of low pathogenic avian influenza virus. CONCLUSION Strengthening the surveillance of AIVs of wild waterfowl and poultry in this region is vital for our knowledge of the ecology and mechanism of transmission to prevent an influenza pandemic.
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Affiliation(s)
- Yi Yao
- Hunan East Dongting Lake National Nature Reserve, Yueyang 414018, Hunan, China
| | - Cui Ling Xu
- National Institute for Viral Disease Control and Prevention, China CDC, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, China
| | - Jing Hong Shi
- National Institute for Viral Disease Control and Prevention, China CDC, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, China
| | - Yun Zhu
- Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - Yun Fei Li
- Hunan East Dongting Lake National Nature Reserve, Yueyang 414018, Hunan, China
| | - Tian Bai
- National Institute for Viral Disease Control and Prevention, China CDC, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, China
| | - Fang Cai Li
- Hunan Provincial Center for Disease Control and Prevention, Changsha 410005, Hunan, China
| | - Tao Cai
- Hunan East Dongting Lake National Nature Reserve, Yueyang 414018, Hunan, China
| | - Fan Yuan
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Tao Chen
- Hunan East Dongting Lake National Nature Reserve, Yueyang 414018, Hunan, China
| | - Hao Yang
- Hunan Provincial Center for Disease Control and Prevention, Changsha 410005, Hunan, China
| | - Wen Chao Li
- Hunan Provincial Center for Disease Control and Prevention, Changsha 410005, Hunan, China
| | - Heng Jiao Zhang
- Hunan Provincial Center for Disease Control and Prevention, Changsha 410005, Hunan, China
| | - Hong Zhang
- Hunan Provincial Center for Disease Control and Prevention, Changsha 410005, Hunan, China
| | - Yue Long Shu
- National Institute for Viral Disease Control and Prevention, China CDC, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, China
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Zlot A, Simckes M, Vines J, Reynolds L, PhD AS, Scott MK, McLuckie JM, Kromer D, Hill VR, Yoder JS, Hlavsa MC. Norovirus outbreak associated with a natural lake used for recreation - Oregon, 2014. MMWR Morb Mortal Wkly Rep 2015; 64:485-90. [PMID: 25974632 PMCID: PMC4584822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In July 2014, Multnomah County public health officials investigated a norovirus outbreak among persons visiting Blue Lake Regional Park in Oregon. During the weekend of the reported illnesses (Friday, July 11-Sunday, July 13) approximately 15,400 persons visited the park. The investigation identified 65 probable and five laboratory-confirmed cases of norovirus infection (70 total cases). No hospitalizations or deaths were reported. Analyses from a retrospective cohort study revealed that swimming at Blue Lake during July 12-13 was significantly associated with illness during July 13-14 (adjusted relative risk = 2.3; 95% confidence interval [CI] = 1.1-64.9). Persons who swam were more than twice as likely to become ill compared with those who did not swim in the lake. To control the outbreak, Blue Lake was closed for 10 days to prevent further illness. This investigation underscores the need for guidance for determining when to reopen untreated recreational water venues (e.g., lakes) associated with outbreaks, and communication tools to inform the public about the risks associated with swimming in untreated recreational water venues and measures that can prevent illness.
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Affiliation(s)
- Amy Zlot
- Multnomah County Health Department
| | - Maayan Simckes
- Multnomah County Health Department
- CDC/CSTE Applied Epidemiology Fellowship Program
| | | | | | | | | | | | - Dan Kromer
- Metro, Blue Lake Regional Park, Fairview, Oregon
| | - Vincent R. Hill
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC
| | - Jonathan S. Yoder
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC
| | - Michele C. Hlavsa
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC
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40
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Butina TV, Potapov SA, Belykh OI, Belikov SI. [Genetic diversity of cyanophages of the Myoviridae family as a constituent of the associated community of the Baikal sponge Lubomirskia baicalensis]. Genetika 2015; 51:384-388. [PMID: 26027378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular-genetic analysis of cyanophages of the family Myoviridae from the associated community of the endemic Baikal sponge Lubomirskia baicalensis was carried out based on the g20 gene fragment. A large cyanophage diversity according to the g20 marker gene was found in the sponge. The Baikal sponge cyanophages were shown to be similar to those inhabiting plankton. Moreover, specific cyanophage groups that are significantly different from all of the known groups inhabiting the Lake Baikal were revealed.
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Palesse S, Colombet J, Pradeep Ram AS, Sime-Ngando T. Linking host prokaryotic physiology to viral lifestyle dynamics in a temperate freshwater lake (Lake Pavin, France). Microb Ecol 2014; 68:740-750. [PMID: 24910014 DOI: 10.1007/s00248-014-0441-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 05/20/2014] [Indexed: 06/03/2023]
Abstract
In aquatic ecosystems, fluctuations in environmental conditions and prokaryotic host physiological states can strongly affect the dynamics of viral life strategies. The influence of prokaryote physiology and environmental factors on viral replication cycles (lytic and lysogeny) was investigated from April to September 2011 at three different strata (epi, meta, and hypolimnion) in the mixolimnion of deep volcanic temperate freshwater Lake Pavin (France). Overall, the euphotic region (epi and metalimnion) was more dynamic and showed significant variation in microbial standing stocks, prokaryotic physiological state, and viral life strategies compared to the aphotic hypolimnion which was stable within sampled months. The prokaryotic host physiology as inferred from the nucleic acid content of prokaryotic cells (high or low nucleic acid) was strongly regulated by the chlorophyll concentration. The predominance of the high nucleic acid (HNA) prokaryotes (cells) over low nucleic acid (LNA) prokaryotes (cells) in the spring (HNA/LNA = 1.2) and vice versa in the summer period (HNA/LNA = 0.4) suggest that the natural prokaryotic communities underwent major shifts in their physiological states during investigated time period. The increase in the percentage of inducible lysogenic prokaryotes in the summer period was associated with the switch in the dominance of LNA over HNA cells, which coincided with the periods of strong resource (nutrient) limitation. This supports the idea that lysogeny represents a maintenance strategy for viruses in unproductive or harsh nutrient/host conditions. A negative correlation of percentage of lysogenic prokaryotes with HNA cell abundance and chlorophyll suggest that lysogenic cycle is closely related to prokaryotic cells which are stressed or starved due to unavailability of resources for its growth and activity. Our results provide support to previous findings that changes in prokaryote physiology are critical for the promotion and establishment of lysogeny in aquatic ecosystems, which are prone to constant environmental fluctuations.
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Affiliation(s)
- S Palesse
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Clermont Université, Université Blaise Pascal, BP 80026, 63171, Aubière Cedex, France
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Butina TV, Potapov SA, Belykh OI, Mukhanov VS, Ryl'kova OA, Damdinsuren N, Chojdash B. [Molecular-and-genetic diversity of cyanophages of the family Myoviridae in Lake Hovsgol (Mongolia)]. Mol Biol (Mosk) 2014; 48:1030-1034. [PMID: 25845244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Cyanophages of the family Myoviridae were studied in Lake Hovsgol based on the analysis of g20 gene fragments. The analysis revealed the diversity of g20 cyanomyovirus sequences in Lake Hovsgol. It was found a great similarity of genes from the Lake Hovsgol and Lake Baikal. Distribution of closely related virus strains in these water bodies is attributed to close geographical location, direct water connection and similar hydrochemical parameters of the lakes.
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ElHadidy AM, Peldszus S, Van Dyke MI. Effect of hydraulically reversible and hydraulically irreversible fouling on the removal of MS2 and φX174 bacteriophage by an ultrafiltration membrane. Water Res 2014; 61:297-307. [PMID: 24967952 DOI: 10.1016/j.watres.2014.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 04/02/2014] [Accepted: 05/03/2014] [Indexed: 05/13/2023]
Abstract
The effect of membrane fouling on the removal of enteric virus surrogates MS2 and φX174 bacteriophage by an ultrafiltration membrane was assessed under simulated full-scale drinking water treatment operating conditions. Filtration experiments of up to 8 days using either river or lake water ascertained how the membrane fouling layer affected virus removal. Organic carbon fractionation techniques identified potential foulants, including biopolymers, in the feed water and in the permeate. Hydraulically irreversible fouling could greatly improve the removal of both viruses at moderate and severe fouling conditions by up to 2.5 logs. Hydraulically reversible fouling increased virus removal only slightly, and increased removal of >0.5 log for both phage were only obtained under severe fouling conditions. The increase in virus removal due to irreversible and reversible fouling differed between the two water sources. As the degree of fouling increased, differences between the removal of the two phage decreased. Maintenance cleaning partially removed membrane foulants, however virus removal following maintenance cleaning was lower than that of the fouled membrane, it remained higher than that of the clean membrane.
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Affiliation(s)
- Ahmed M ElHadidy
- NSERC Chair in Water Treatment, Department of Civil and Environmental Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.
| | - Sigrid Peldszus
- NSERC Chair in Water Treatment, Department of Civil and Environmental Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Michele I Van Dyke
- NSERC Chair in Water Treatment, Department of Civil and Environmental Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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Guerrini L, Paul MC, Leger L, Andriamanivo HR, Maminiaina OF, Jourdan M, Molia S, Rakotondravao R, Chevalier V. Landscape attributes driving avian influenza virus circulation in the Lake Alaotra region of Madagascar. Geospat Health 2014; 8:445-453. [PMID: 24893021 DOI: 10.4081/gh.2014.33] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
While the spatial pattern of the highly pathogenic avian influenza H5N1 virus has been studied throughout Southeast Asia, little is known on the spatial risk factors for avian influenza in Africa. In the present paper, we combined serological data from poultry and remotely sensed environmental factors in the Lake Alaotra region of Madagascar to explore for any association between avian influenza and landscape variables. Serological data from cross-sectional surveys carried out on poultry in 2008 and 2009 were examined together with a Landsat 7 satellite image analysed using supervised classification. The dominant landscape features in a 1-km buffer around farmhouses and distance to the closest water body were extracted. A total of 1,038 individual bird blood samples emanating from 241 flocks were analysed, and the association between avian influenza seroprevalence and these landcape variables was quantified using logistic regression models. No evidence of the presence of H5 or H7 avian influenza subtypes was found, suggesting that only low pathogenic avian influenza (LPAI) circulated. Three predominant land cover classes were identified around the poultry farms: grassland savannah, rice paddy fields and wetlands. A significant negative relationship was found between LPAI seroprevalence and distance to the closest body of water. We also found that LPAI seroprevalence was higher in farms characterised by predominant wetlands or rice landscapes than in those surrounded by dry savannah. Results from this study suggest that if highly pathogenic avian influenza H5N1 virus were introduced in Madagascar, the environmental conditions that prevail in Lake Alaotra region may allow the virus to spread and persist.
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Lee CS, Lee C, Marion J, Wang Q, Saif L, Lee J. Occurrence of human enteric viruses at freshwater beaches during swimming season and its link to water inflow. Sci Total Environ 2014; 472:757-66. [PMID: 24333998 DOI: 10.1016/j.scitotenv.2013.11.088] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 11/09/2013] [Accepted: 11/18/2013] [Indexed: 05/27/2023]
Abstract
Human enteric viruses are significant etiological agents for many recreational waterborne illnesses. The occurrence and density of human enteric viruses such as human adenovirus (HAdV), human enterovirus (HEnV), and human norovirus genogroups I/II (HNoV GI/GII) were investigated using quantitative real-time PCR (qPCR) at freshwater beaches along with monitoring fecal indicators and environmental parameters. During the 2009 swimming season, water samples were collected from three inland freshwater beaches in Ohio, USA. Of the total samples, 40% (26/65) and 17% (11/65) were positive for HAdV and HEnV respectively, but HNoV GI/GII were not detected. There was no significant association among the detected human enteric viruses (HAdV and HEnV) and fecal bacteria indicators (Escherichia coli and Bacteroides) by Spearman correlation and principal component analyses. Logistic regression analysis also revealed that the odds of finding HAdV or HEnV was not influenced by levels of fecal bacteria indicators. However, there was a 14-fold increase in the odds of HEnV detection for each 1-log increase in daily water inflow (m(3)/s) into freshwater beach reservoirs (adjusted odds ratio=14.2; 95% confidence interval=1.19-171). In summary, the viral occurrence at the freshwater beaches was not readily explained by the levels of fecal bacteria indicators, but appeared to be more related to water reservoir inflows. These results suggest that hydrological data must be considered in future epidemiology efforts aimed at characterizing beach water safety.
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Affiliation(s)
- Chang Soo Lee
- College of Public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Cheonghoon Lee
- College of Public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Jason Marion
- College of Public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Qiuhong Wang
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691, USA
| | - Linda Saif
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691, USA
| | - Jiyoung Lee
- College of Public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA; Department of Food Sciences & Technology, The Ohio State University, Columbus, OH 43210, USA.
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Zhong X, Ram ASP, Colombet J, Jacquet S. Variations in abundance, genome size, morphology, and functional role of the virioplankton in Lakes Annecy and Bourget over a 1-year period. Microb Ecol 2014; 67:66-82. [PMID: 24253662 DOI: 10.1007/s00248-013-0320-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 10/24/2013] [Indexed: 06/02/2023]
Abstract
We sampled the surface waters (2-50 m) of two deep peri-alpine lakes over a 1-year period in order to examine (1) the abundance, vertical distribution, genome size, and morphology structures of the virioplankton; (2) the virus-mediated bacterial mortality; and (3) the specific genome size range of double-stranded DNA (dsDNA) phytoplankton viruses. Virus-like particle (VLP) concentrations varied between 4.16 × 10(7) (January) and 2.08 × 10(8) part mL(-1) (May) in Lake Bourget and between 2.7 × 10(7) (June) and 8.39 × 10(7) part mL(-1) (November) in Lake Annecy. Our flow cytometry analysis revealed at least three viral groups (referred to as virus-like particles 1, 2, and 3) that exhibited distinctive dynamics suggestive of different host types. Phage-induced bacterial mortality varied between 6.1% (June) and 33.2% (October) in Lake Bourget and between 7.4% (June) and 52.6% (November) in Lake Annecy, suggesting that viral lysis may be a key cause of mortality of the bacterioplankton. Virioplankton genome size ranged from 27 to 486 kb in Lake Bourget, while it reached 620 kb in Lake Annecy for which larger genome sizes were recorded. Our analysis of pulsed field gel electrophoresis bands using different PCR primers targeting both cyanophages and algal viruses showed that (1) dsDNA viruses infecting phytoplankton may range from 65 to 486 kb, and (2) both cyanophage and algal "diversity" were higher in Lake Annecy. Lakes Annecy and Bourget also differed regarding the proportions of both viral families (with the dominance of myoviruses vs. podoviruses) and infected bacterial morphotypes (short rods vs. elongated rods), in each of these lakes, respectively. Overall, our results reveal that (1) viruses displayed distinct temporal and vertical distribution, dynamics, community structure in terms of genome size and morphology, and viral activity in the two lakes; (2) the Myoviridae seemed to be the main cause of bacterial mortality in both lakes and this group seemed to be related to VLP2; and (3) phytoplankton viruses may have a broader range of genome size than previously thought. This study adds to growing evidence that viruses are diverse and play a significant role in freshwater microbial dynamics and more globally lake functioning. It highlights the importance of further considering this biological compartment for a better understanding of plankton ecology in peri-alpine lakes.
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Affiliation(s)
- Xu Zhong
- INRA, UMR 042 CARRTEL, 75 Avenue de Corzent, 74203, Thonon-les-Bains cx, France
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Jing R, Kimura M, Wang G. [Genetic diversity of capsid assembly protein genes (g20) of cyanophage in different natural environment--a review]. Wei Sheng Wu Xue Bao 2013; 53:1149-1157. [PMID: 24617255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
With the development of molecular biological techniques and progress of sequencing virus genome, scientists pay great attentions to the genetic diversity of viruses, which are ubiquitous and abundant in natural environments. So far, no universal genetic marker, analogous to 16S rDNA and 18S rDNA used for microbial communities exists throughout all viruses. However, some family-specific genes encoding conserved amino acids have been proposed for the evaluation of phage diversity and a series of breakthrough achievements were obtained. In this paper, we targeted the capsid assembly protein genes (g20) of cyanophages and reviewed the recent progress on their genetic diversity in natural environments of marines, lakes and paddy fields and discussed the relationship between distribution of g20 gene of cyanophages and its environments. Those studies showed that the distribution of g20 gene varied with environments and many unique clusters were found in different natural environment. In final, several research issues and the future research tendencies for the study of environmental g20 gene were also addressed in this paper.
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48
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Ram ASP, Palesse S, Colombet J, Sabart M, Perriere F, Sime-Ngando T. Variable viral and grazer control of prokaryotic growth efficiency in temperate freshwater lakes (French Massif Central). Microb Ecol 2013; 66:906-916. [PMID: 24061344 DOI: 10.1007/s00248-013-0289-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 09/03/2013] [Indexed: 06/02/2023]
Abstract
The effects of viral lysis and heterotrophic nanoflagellate grazing (top down forces) on prokaryotic mortality and their subsequent impact on their metabolism were estimated in the upper euphotic and deeper aphotic depth of 11 freshwater lakes located in the French Massif Central. The standing stocks of viruses (VA) and heterotrophic nanoflagellate (HNF) varied significantly (p < 0.05) with sampled depth. VA was substantially (twofold on an average) and significantly higher (p < 0.03) at the aphotic compared to euphotic depth, whereas the reverse was true (p < 0.02) for HNF. Among the prokaryote subgroup, high nucleic acid content prokaryotes explained for significant variability in the total VA and served as principle host target for viral proliferation. Like standing stocks, flagellate grazing and viral infection rates also followed similar patterns. In the investigated lakes, the mechanism for regulating prokaryotic production varied with sampled depth from grazing control in the euphotic to control due to viral lysis in the aphotic. We also tested the hypothesis of top down control on prokaryotic growth efficiency (PGE, which we used as an index of prokaryotic physiological and energetic status at the community level) at both depths. Overall, among the studied lakes, PGE varied widely (4-51 %) with significantly (p < 0.05) lower values in the aphotic (mean = 18 ± 4 %) than euphotic depth (mean = 32 ± 9 %). Contrasting observations on the top down control of PGE between sampled depths were observed. The presence of grazers was found to stimulate PGE at the euphotic, whereas viruses through their lytic infection had a strong negative impact on PGE at the aphotic depth. Such observed differences in PGE and the mechanism controlling prokaryotic production with depth could eventually have strong implication on carbon and nutrient flux patterns in the studied lakes.
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Affiliation(s)
- A S Pradeep Ram
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Clermont Université, Université Blaise Pascal, BP 80026, 63171, Aubiere Cedex, France,
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Colombet J, Sime-Ngando T. Seasonal depth-related gradients in virioplankton: lytic activity and comparison with protistan grazing potential in Lake Pavin (France). Microb Ecol 2012; 64:67-78. [PMID: 22391799 DOI: 10.1007/s00248-012-0032-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 02/17/2012] [Indexed: 05/31/2023]
Abstract
This study presents an original depth-related survey of virioplankton lytic activity in relation to prokaryotic production and potential protistan bacterivory in the deep (Z(max) = 92 m) meromictic volcanic Lake Pavin (Massif Central, France). The sampling strategy was designed to be representative of the physico-chemical gradients of the water column of the lake, and of the seasonal variability as well, i.e. 12 different depths sampled in triplicates from April to December 2005. In the space, viral lytic activity estimated from the frequency of visibly infected prokaryotic cells and from burst size over the study period generally decreased with depth. This was viewed as a paradox compared to the abundances of viruses and prokaryotes and to the prokaryotic production which increased with depth. The seasonal variability in viral lytic activity was correlated with prokaryotic variables (abundance and production) in the deepest waters, i.e. from the hypolimnion downwards. Compared to previous studies known from the mixolimnion, we conclude that the deep waters in Lake Pavin represent an exclusive environment for heterotrophic prokaryotes whose seasonal activity offers an optimal and unique resource for thriving viral communities, some of which may be typical, endemic to the ambient dark, cold and stable deep water masses. Overall, the main findings in the present study get well around a previous statement that the ecology of the deepest waters of Lake Pavin is essentially driven by the dark viral loop (dissolved organic matter-prokaryotes-viruses) processes, which can sequester organic matters and nutrients for a long-lived turnover time. This is in agreement with recent demonstrations from marine systems that meso- and bathypelagic waters are optimal environments for viral survival and proliferation.
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Affiliation(s)
- Jonathan Colombet
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université Blaise Pascal, UMR CNRS 6023, Aubière, France
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Roux S, Enault F, Robin A, Ravet V, Personnic S, Theil S, Colombet J, Sime-Ngando T, Debroas D. Assessing the diversity and specificity of two freshwater viral communities through metagenomics. PLoS One 2012; 7:e33641. [PMID: 22432038 PMCID: PMC3303852 DOI: 10.1371/journal.pone.0033641] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 02/14/2012] [Indexed: 01/21/2023] Open
Abstract
Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale. To help identify the characteristics and potential specificities of freshwater viral communities, such communities from two lakes differing by their ecological parameters were studied through metagenomics. Both the cluster richness and the species richness of the Lake Bourget virome were significantly higher that those of the Lake Pavin, highlighting a trend similar to the one observed for microorganisms (i.e. the specie richness observed in mesotrophic lakes is greater than the one observed in oligotrophic lakes). Using 29 previously published viromes, the cluster richness was shown to vary between different environment types and appeared significantly higher in marine ecosystems than in other biomes. Furthermore, significant genetic similarity between viral communities of related environments was highlighted as freshwater, marine and hypersaline environments were separated from each other despite the vast geographical distances between sample locations within each of these biomes. An automated phylogeny procedure was then applied to marker genes of the major families of single-stranded (Microviridae, Circoviridae, Nanoviridae) and double-stranded (Caudovirales) DNA viruses. These phylogenetic analyses all spotlighted a very broad diversity and previously unknown clades undetectable by PCR analysis, clades that gathered sequences from the two lakes. Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes. Furthermore, freshwater viral communities appear genetically distinct from other aquatic ecosystems, demonstrating the specificity of freshwater viruses at a community scale for the first time.
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Affiliation(s)
- Simon Roux
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Francois Enault
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
- * E-mail:
| | - Agnès Robin
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Viviane Ravet
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Sébastien Personnic
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Sébastien Theil
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Jonathan Colombet
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Télesphore Sime-Ngando
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Didier Debroas
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
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