Development of a high throughput technology for detecting virus infection and immunity in the natural environment
Lead Research Organisation:
NERC CEH (Up to 30.11.2019)
Department Name: Hails
Abstract
This proposal is to prove the concept and develop a high throughput methodology for screening virus infections and immunities in wild plant and insect communities. We propose to obtain small RNA profiles of the plant and insect communities from the Wytham Wood, Oxfordshire, by using Solexa high throughput sequencing. The anti-virus small interfering (avsi)RNAs that are produced by the host gene silencing systems against the virus RNAs will be screened for viral origins. We anticipate the detection of the avsiRNAs against the known prevalent viruses at the site and will use these viruses as positive controls to optimize conditions of sample preparation, sequencing, and bioinformatics. We also expect to discover the prevalence of previously unconfirmed and unknown viruses, and we plan to validate these newly detected infections by using the conventional methods (e.g., RTPCR, cloning and sequencing, Northern Blotting, etc.) to determine the sensitivity and accuracy of the high throughput methodology. To enable the conventional method assessment, we plan to label samples for each sampled species by using sequence tags. The sampling regime is designed for achieving a sensitivity of shotgun detection of 5% infection rate for plant populations. The tagged samples will be pooled together for high throughput sequencing runs to achieve cost effectiveness. The resulting sequences will be sorted back to their original sample identities and analyzed. Results will be validated by using the conventional methods with the sorted specific samples. Mass post-sequencing analyses will also be performed without sorting the samples to their original identities. Results from the specific analyses and mass analyses will be compared. The mass analyses without the requirement of sorting samples are designed for testing a capacity of genetic random sampling from an ecosystem without restriction of sampling regimes. The technology will offer a broad range of applications from large scale random sampling in natural conditions during the environment change, to defined survey in agricultural and the other managed conditions.
People |
ORCID iD |
Hui Wang (Principal Investigator) | |
Robert Possee (Co-Investigator) |
Publications
Malham SK
(2014)
The interaction of human microbial pathogens, particulate material and nutrients in estuarine environments and their impacts on recreational and shellfish waters.
in Environmental science. Processes & impacts
Fan C
(2013)
Selection of reference genes for quantitative real-time PCR in bamboo (Phyllostachys edulis).
in PloS one
Wang Y
(2014)
A survey of overlooked viral infections in biological experiment systems.
in PloS one
Gao S
(2014)
Applications of RNA interference high-throughput screening technology in cancer biology and virology.
in Protein & cell
Zhou C
(2018)
Characterization of viral RNA splicing using whole-transcriptome datasets from host species.
in Scientific reports
Ma J
(2015)
Mutational bias of Turnip Yellow Mosaic Virus in the context of host anti-viral gene silencing.
in Virology
Description | We developed a sequence homology based virus searching strategy to detect virus infections from field collected plant and insect samples. |
Exploitation Route | The work has been published and has been used/cited by the other scientists. |
Sectors | Agriculture Food and Drink Digital/Communication/Information Technologies (including Software) Environment Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
Description | International Collaboration Research |
Amount | ¥1,700,000 (CNY) |
Funding ID | Collaboration research on human-related environmental microbiology using next generation sequencing technology (2011DFA33220) |
Organisation | Ministry of Science and Technology |
Sector | Public |
Country | China |
Start | 03/2012 |
End | 03/2015 |
Description | Overseas Collaboration Research |
Amount | ¥200,000 (CNY) |
Funding ID | Small RNA investigation on the relationship of virus immunity and bamboo flowering (31028004) |
Organisation | National Science Foundation China |
Sector | Public |
Country | China |
Start | 01/2011 |
End | 12/2012 |