DNAiTECH:in-field DNA testing
Why test for DNA in the field?
There are obvious benefits to be able to perform a DNA analysis immediately on-site when and where it is needed. For environmental testing, the terminology is in-field testing, for clinical concerns it is termed point-of-care testing or POCT. Such testing is indeed the holy grail of molecular diagnostics. Rapid verification of disease, infection, or contamination enhances the efficacy of first response, saving lives, preventing disease spread, enabling preemptive isolation of affected individuals or animals or diseased crops, providing an early warning when there are toxins or disease-causing pathogens present in the environment. Yet everyday molecular diagnostics require expensive instrumentation operated by technologists within specialized laboratory facilities; to deliver such tests outside the lab presents significant challenges.
W.H.O. guidelines for in-field POC testing?
Health solutions are disproportionately first world focused, the high costs of test development, and the economic imperatives favor a system where non-first world humanitarian health solutions are low priority. Technological solutions must also benefit the lives of those who live with extremes of poverty. To deliver an in-field test that can be used to benefit poor communities, where there is minimal infrastructure, requires demanding test specifications. The World Health Organisation defines the criteria for an ideal humanitarian POCT with the acronym ASSURED which stands for Affordable, Sensitive, Specific, User-friendly, Robust & Rapid, Equipment-free, and Deliverable[i]. The same criteria apply to critical in-field environmental testing and also for agritech applications.
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Smartphones for DNA testing
DNA based diagnostics are powerful tools for in-field and POCT, and applicable for resource-limited situations if there is the availability of suitable portable low energy instrumentation, robust chemistries, and if the process is simple, user-friendly and data interpretation straight forward. Recent publications explore different ways to use mobile phone-based DNA sensors to reduce instrument complexity and cost for in-field POCT applications[i] [ii] [iii] [iv] [v].
Suitable chemistry for in-field DNA testing
The chemistry for amplifying the DNA or RNA are another key aspect for viable applications, it must be robust, cheap, and packaged in a way so it works without laboratory infrastructure and refrigeration. It is well established that isothermal DNA amplification chemistries are much more suitable for nucleic acid amplification than standard PCR thermocycling chemistries, the DNA amplifying enzymes are often less fussy as to the target DNA’s purity and the energy requirements for the instruments is much lower when amplification occurs at a single temperature[i].
DNAiTECH, an in-field capable package
DNAiTECH was developed for in-field and POC applications. The low cost of the instrument, the robustness of the LAMP chemistry, the low cost of reagents, minimal power requirement and battery operation, the ubiquitous availability of smartphones and the ease of implementation means there is great potential for many types of tests to be developed fulfilling all or most of the WHO POCT criteria. The DNAiTECH is a complete laboratory free package, suitable for classroom and in-field testing. We have developed a DNA extraction process using magnetic particles and a tube rack with a magnetic strip to purify the DNA, this avoids the need for centrifugation in-field or hazardous solvents or extraction kits. Freeze-dried reagent master mixes and calibration standards enable the user to implement a test with only minimal dispensing of reaction components. Technologies like DNAiTECH may help to play an important role in delivering a more equitable and ethical health system prioritizing all humanity irrespective of socioeconomic circumstances.
Above: A rapid yes/no test for the anatoxin C producing cyanobacteria M. autumnalis. Different environmental samples were tested using the DNAiTECH and the LAMP assay for Ana C. Two of the river samples were strongly positive.
DNAiTECH tests, now and the future
E. coli testing:
E. coli is the internationally recognized marker for fecal contamination of waterways. With the New Zealand Governments 2017 pledge to make 90% of our waterways swimmable by 2040 [i], there is an increased obligation on regional authorities to monitor and provide solutions for enhancing the quality of their local waterways. The availability of tests that can be implemented in the field, can enable faster detection, improved coordination to identify the exact source and more rapid closure of waterways for health & safety when contamination occurs.
M. autumnalis testing:
Toxic cyanobacteria contamination of waterways in New Zealand is increasingly becoming a problem, factors such as increased nitrogen load, loss of riparian margins, effluent infiltration from agriculture and towns and climatic changes have led to a rise in anatoxin C producing organisms in many rivers within New Zealand[ii]. The toxin is lethal to dogs when the algal mass is consumed.
New LAMP-based tests are being developed to be used with the DNAiTECH instrument. We are looking at rapid diagnostic pathogen detection within the viticulture and apiculture industries as well as environmental applications.