JoVE Logo
Faculty Resource Center

Sign In

Summary

Abstract

Introduction

Protocol

Representative Results

Discussion

Acknowledgements

Materials

References

Immunology and Infection

A Rapid Strategy for the Isolation of New Faustoviruses from Environmental Samples Using Vermamoeba vermiformis

Published: June 4th, 2016

DOI:

10.3791/54104

1Faculty of Medicine and Pharmacy, Research Unit for Infectious and Tropical Emerging Diseases, Aix Marseille University, 2Pole of Infectious and Tropical Diseases, Clinical and Biological Sector, Federation of Bacteriology-Hygiene Virology, University Hospital Institute Mediterranean Infection

We describe here the latest advances in viral isolation for the characterization of new genotypes of Faustovirus, a new asfarvirus-related lineage of giant viruses. This protocol can be applied to the high throughput isolation of viruses, especially giant viruses infecting amoeba.

The isolation of giant viruses is of great interest in this new era of virology, especially since these giant viruses are related to protists. Giant viruses may be potentially pathogenic for many species of protists. They belong to the recently described order of Megavirales. The new lineage Faustovirus that has been isolated from sewage samples is distantly related to the mammalian pathogen African swine fever virus. This virus is also specific to its amoebal host, Vermamoeba vermiformis, a protist common in health care water systems. It is crucial to continue isolating new Faustovirus genotypes in order to enlarge its genotype collection and study its pan-genome. We developed new strategies for the isolation of additional strains by improving the use of antibiotic and antifungal combinations in order to avoid bacterial and fungal contaminations of the amoeba co-culture and favoring the virus multiplication. We also implemented a new starvation medium to maintain V. vermiformis in optimal conditions for viruses co-culture. Finally, we used flow cytometry rather than microscopic observation, which is time-consuming, to detect the cytopathogenic effect. We obtained two isolates from sewage samples, proving the efficiency of this method and thus widening the collection of Faustoviruses, to better understand their environment, host specificity and genetic content.

The discovery of giant viruses, especially those belonging to the Megavirales order, completely changed the world of viruses in terms of particle size and genome complexity. Viruses were previously thought to be small entities, and the Mimivirus appeared to break all the rules.1 Metagenomic data suggests the ubiquity of giant viruses not only in the environment, 2-5 but also in humans.6 Therefore, there is still a need to search for these viruses on a large scale. The diversity of these giant viruses was assessed by sampling not only a variety of aquatic environments and their associated sediments worldwide,7-11 but also by ....

Log in or to access full content. Learn more about your institution’s access to JoVE content here

1. Sample Collection

  1. Collect 70 samples from different environments and regions. In this case, use the following: 5 dirty water samples from the village of Saint Pierre de Meyzoargues (France), 15 samples from the lake in Parc Borély in Marseille (France); 15 sea water samples with sediment from the rocky inlets at Samena in Marseille (France), 25 river water samples from the Alps (France), and finally, 10 samples from sewage in La Ciotat (France).
  2. Vortex samples for homogenization before inocu.......

Log in or to access full content. Learn more about your institution’s access to JoVE content here

The system studied in this manuscript validated its proof of concept by isolating two new Faustoviruses. Of the 70 samples tested, two episodes of lysis were detected, in contrast to our reliable negative controls. The negative control for lysis contained an 86% amoeba population. By contrast, the positive samples (ST1 for Saint Pierre de Meyzoargues), and (LC9 for the La Ciotat Sample 9) showed a dramatic decline in gated amoebae; more than 60% of amoebae were lysed with the highest perc.......

Log in or to access full content. Learn more about your institution’s access to JoVE content here

The possibility that Faustovirus could be the first member of a new Megavirales family close to ASFV was first suggested by Reteno et al.,19 but some differences can still be distinguished. It appears unclear whether Faustovirus should join the Asfarviridae family or whether it should instead form a new putative viral family. This issue will require further investigation, in particular a more comprehensive characterization of its morphology, host range, replication cycle and gene repertoire. More Faus.......

Log in or to access full content. Learn more about your institution’s access to JoVE content here

The authors have no acknowledgements to make.

....

Log in or to access full content. Learn more about your institution’s access to JoVE content here

Name Company Catalog Number Comments
LSR FORTESSA cytometer  BD Biosciences France  649225B4
TECNAI G2 F20 FEI Germany  5027/11
Optical inverted microscope leica  France 72643
DNA extraction Qiagen EZ1 Advanced XL Extraction Robot France  L106A0452
PCR Cycler CFX96 Bio rad France 785BR06298
PYG medium , PAS, Starvation medium In house laboratory production  Marseille URMITE x
Amoeba strain CDC-19 ATCC France 50237
Plates Cellstar France 655180
PCR materials, primers.  eurogentec France Primers cited in manuscript
glasstic slide 10 with grids Kova  USA H899871441F
Eosin/ blue Azur-Hemacolor stain Merck milipore  France 111955,6,57,109468
Vacuum driven filters Thermo scientific France BPV4550 / 20170115
Phosphate-Buffered Saline Thermo Fisher scientific  France  10010-023
DAPI stain Life Technologies  France  D1306
cytospin  4 cytocentrifuge Thermo Fisher scientific  France  10522013JT184-31
Single cytology tunnel Biomedical polymers inc. France BMP-cyto-S50
Carbon grids  Euromedex France  FCF400NI
Ammonium molibdate VWR internationanl  France  21276185
Flasks  SARSTEDT Germany 833911
0.22μm filters  Milex millipor  France SE2M229104
Ultracentrifuge Sorval WX 80 Thermo scientific France 9102448
Rapid-flow filters Nalgene France 450-0020

  1. Raoult, D., et al. The 1.2-megabase genome sequence of Mimivirus. Science. 306 (5700), 1344-1350 (2004).
  2. Claverie, J. -. M. Giant viruses in the oceans: the 4th Algal Virus Workshop. Virol J. 2, 52-52 (2004).
  3. Monier, A. A., et al. Marine mimivirus relatives are probably large algal viruses. Audio, Transactions of the IRE Professional Group on. 5, 12-12 (2007).
  4. Monier, A., Claverie, J. M., Ogata, H. Taxonomic distribution of large DNA viruses in the sea. Genome Biol. , (2008).
  5. Claverie, J. -. M., et al. Mimivirus and Mimiviridae: Giant viruses with an increasing number of potential hosts, including corals and sponges. J Invertebr Pathol. 101 (3), 9-9 (2009).
  6. Colson, P., et al. Evidence of the megavirome in humans. J Clin Virol. 57 (3), 191-200 (2013).
  7. La Scola, B., et al. Tentative characterization of new environmental giant viruses by MALDI-TOF mass spectrometry. Intervirology. 53 (5), 344-353 (2010).
  8. Boughalmi, M., et al. High-throughput isolation of giant viruses of the Mimiviridae and Marseilleviridae families in the Tunisian environment. Environ Microbiol. , (2012).
  9. Pagnier, I., et al. A decade of improvements in mimiviridae and marseilleviridae isolation from amoeba. Intervirology. 56 (6), 354-363 (2012).
  10. Philippe, N., et al. Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes. Science. 341 (6143), 281-286 (2013).
  11. Legendre, M., et al. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. PNAS. , (2014).
  12. Saadi, H., et al. First Isolation of Mimivirus in a Patient With Pneumonia. Clin Infect Dis. , (2013).
  13. Saadi, H., et al. Shan virus: a new mimivirus isolated from the stool of a Tunisian patient with pneumonia. Intervirology. 56 (6), 424-429 (2013).
  14. Claverie, J. -. M., Abergel, C. Mimivirus: the emerging paradox of quasi-autonomous viruses. Trends Genet : TIG. 26 (10), 431-437 (2010).
  15. Colson, P., et al. Viruses with more than 1,000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes. Genome Biol Evol. 3, 737-742 (2010).
  16. Claverie, J. -. M., Abergel, C. Open questions about giant viruses. Adv Virus Res. 85, 25-56 (2013).
  17. Fischer, M. G. M., Allen, M. J. M., Wilson, W. H. W., Suttle, C. A. C. Giant virus with a remarkable complement of genes infects marine zooplankton. PNAS. 107 (45), 19508-19513 (2010).
  18. Van Etten, J. L. Another really, really big virus. Viruses. 3 (1), 32-46 (2011).
  19. Reteno, D. G., et al. Faustovirus, an asfarvirus-related new lineage of giant viruses infecting amoebae. J.Virol. , (2015).
  20. Coşkun, K. A., Ozçelik, S., Tutar, L., Elaldı, N., Tutar, Y. Isolation and identification of free-living amoebae from tap water in Sivas, Turkey. Biomed res Int. 2013, 675145 (2013).
  21. Bradbury, R. S. Free-living amoebae recovered from human stool samples in Strongyloides agar culture. J Clin microbiol. 52 (2), 699-700 (2014).
  22. Pagnier, I., Valles, C., Raoult, D., La Scola, B. Isolation of Vermamoeba vermiformis and associated bacteria in hospital water. Microb Pathog. 80, 14-20 (2015).
  23. Ogata, H., Toyoda, K., et al. Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus. Virol J. 6, 178-178 (2008).
  24. Tarutani, K., Nagasaki, K., Itakura, S. Isolation of a virus infecting the novel shellfish-killing dinoflagellate Heterocapsa circularisquama. Aquat Microb Ecol. 23, 103-111 (2001).

This article has been published

Video Coming Soon

JoVE Logo

Privacy

Terms of Use

Policies

Research

Education

ABOUT JoVE

Copyright © 2024 MyJoVE Corporation. All rights reserved