In March of this year, even though there were no diagnosed cases of Covid-19 in Valdivia and with only the first infected in Chile, a team of researchers from the Faculties of Veterinary Sciences, Medicine, Sciences and the Center for Genomics and Biotechnology of the Southern University of Chile, decided to meet to contribute and seek some solution to this pandemic. This is how they began to work on proposing an initiative that not only innovates in its test form, but also allows to generate a model of disease surveillance, replicable anywhere in Chile.
The project has already completed its three stages: the first was to validate the sampling technique, individually and grouply; the second to apply it in a pilot plan, in which 450 people were tested, and the third generate a «workflow model», to understand the requirements for a massive Coronavirus surveillance model that can be replicated elsewhere.
«This also involves knowing the costs associated with this program, and the volumes of samples with the equipment available, which in our case we can analyze 17,500 people monthly,» said Claudio Verdugo, director of the Disease Ecology Laboratory of the U. Austral of Chile and project leader.
Innovation in virus detection technique
Analyzing the test currently used as an officer (qPCR – TaqMan), the researchers assessed that in terms of cost and efficiency «due to high demand, in the medium term the necessary inputs are expected to be scarce, so we have validated an alternative form of viral detection,» Verdugo said. However, the Covid-19 virus can be detected through the official test, which uses fluorescent probe, but also that there is another option using fluorescent stains.
This is how they validated this detection technique in individual samples by proving that, in terms of sensitivity, both methods are very similar, with the price difference. «Fluorescent staining, which we are testing, is recognized for being an economical technique and has been used for many years,» he says. On the other hand, he emphasized that this type of techniques, both by fluorescent probe and fluorescent staining, is something that epidemiologists know very well, know the advantages and disadvantages of each and is something that they usually use in the search for diseases of populations in animals.
What they did was to use these same techniques, but in a human pandemic, obtaining the positive results «the clinical and analytical sensitivity of the fluorescent staining test so far is similar, to the sensitivity of TaqMan (official fluorescent probe test), that is, if we correlate the results of both tests, they are 100% equal».
Testing in Pooling: Faster and 10 times cheaper
The reasons that led the UACh team to seek an alternative mass testing technique was that currently testing is individual and therefore expensive. One of the objectives of his project was to validate a method of group or pool testing. In this way, the general population, such as asymptomatic, pre-symptomatic, and people at high risk of becoming infected, is tested. This is how in phase two of the initiative, after validating two different detection techniques, they validated with both techniques a method of mass testing in groups of 5, 10 and 20 samples.
«If our focus is asymptomatic and presymptomatic, most samples will come back negative, so analyzing individually is inefficient in costs and time,» explained the U. Austral epidemiologist.
Also, Verdugo explained that pool means that you can analyze five or 10 individuals in a single reaction, «significantly reducing costs and time. We have calculated that it can be up to 10 times cheaper than sampling individually. Only if a pool is positive, do you individually analyze those samples from that group separately,» explains Verdugo.
Validation in pilot program
To validate the sample outside the lab, the scientists tested the technique in a pilot plan. «We use both the official and the alternative techniques, first individually and then in pool, subject to approval by the scientific ethics committee. Then we showed staff of the Chilean Army and health personnel from all hospitals in the Los Ríos Region, who at least had a confirmed case of Covid-19. In total there were 450 people at risk of infection because of the high degree of exposure and critical roles they perform,» said the research team leader.
Funding for the project was obtained through the Regional Government of the Los Ríos region and the Universidad Austral de Chile through the Vice-Chancellorship of Research, Innovation and Artistic Creation (VIDCA) and the Faculty of Veterinary Sciences.
It should be noted that the three stages of this initiative were implemented in a very short time, from the time the financial contributions were received until the completion of the pilot, which was between April 16 and May 12.
Covid-19 Mass Epidemiological Surveillance Model
The third and most relevant objective is that the pilot plan allowed to validate and optimize the techniques and decide on the most cost-effective, to generate a surveillance flow model of the Covid-19.
«In this plan I want to emphasize that the idea is not to replace the current technique of the symptomatic sick, but is to leave the hospital-sick axis and monitor people at risk, but in a massive way, this with the aim of controlling the virus first, and then, in a post-peak stage or de-escalation of crisis, to manage to establish zones free of contagion,» Verdugo explained.
«More than 50% of people are asymptomatic so an effective, cheap, fast and massive tool is needed to detect and isolate the sick and in this sense our proposal, to work with this alternative technique and in pool is a very good solution,» he added.
At the same time Executioner said that in this surveillance system we set the criteria for those who need to be tested and monitored as a priority to avoid saturation of health systems. «The risk of children, those of an older adult center, or a prison or family members of health staff is very different. And that’s why we set criteria, and what is the sampling pressure needed in each one so that this model can be replicable anywhere else.»
«We know what laboratory equipment and supplies are needed, how many staff, to whom it takes to test, and how much it costs,» he concluded.
The seremi of Science, Technology and Knowledge, of the Region of Los Ríos, Dr. Olga Barbosa, highlighted the project. «Researchers used these techniques, but in animal disease ecology and managed to adapt it for humans to diagnose COVID-19 and that’s innovation. In addition to that they did it in record time,» he said
He also stressed the low cost and importance of the mass diagnosis they propose, stating that, «this allows to reach more people, something that in Chile has not yet been done. While the government has expanded those it must diagnose, it is not being done in a massive way, and that is something that in other countries is being tested and really works.»
For his part, Vice-Chancellor Hans Richter, of the Vice-Chancellor of Research, Development and Artistic Creation, noted that it is «a project that allows us to become independent of the international diagnostic supply chain, showing that at the country level we are able to innovate in concrete solutions of the first level and that it would benefit not only the region but the whole of Chile since the surveillance program they propose allows it to be replicable and scalable».
Recently the research was published a scientific paper with the results found in the following link.