In the worst of the third wave, Spain only sequenced 0.078% of the samples of patients infected by coronavirus: it was like trying to know the dimensions of a huge iceberg using only the palm of one hand. The country is now putting in place an epidemiological surveillance system to analyze random sectors of the population and find out the real prevalence of the British variant and other worrisome ones such as the Brazilian or South African. Several systems, some already commercial, others under development, could speed up this task in the face of the possibility of a fourth wave.
"The epidemiological surveillance of the new variants is more important than ever" Iñaki Comas, geneticist
A recently published study describes a new rapid diagnostic system that could be part of the solution in the fight against new variants. It has been designed by the team of researcher Juan Carlos Izpisua at the Salk Institute in California with the idea of getting a quick and inexpensive way to know if someone is infected and with what variant.
"This method is cheap and practical," explains Izpisua. “The operator does not have to have any previous experience, just put the biological sample in a tube. It could be in any emergency department of a hospital or take it to any place, residences, schools, and have a quick and accurate assessment of the pathogens present in a given community without any special infrastructure ”, he adds.
Currently, diagnoses they are made with a PCR machine that takes just over two hours. Then the complete genome of the virus found in each patient must be sequenced. Both systems are very reliable and provide a large amount of information
The prototype designed by the Izpisua team does a less meticulous job, but in return it is very fast. It fits in a briefcase and consists of a quick test that can analyze samples from 96 patients at a time and tell if they are infected in 15 minutes. The system incorporates a pocket genetic sequencer. This device does not read the complete genome of the virus, which has 30,000 letters, but only specific parts where the mutations that characterize each variant are found, in this case the British one. Sequencing takes just over three hours, bringing the full analysis time to about three and a half hours, much less than what it usually takes using PCR and conventional sequencers. The details of the system have been published in the journal Med .
This device would join others that already exist on the market and that have been key in the monitoring of new variants. A method developed by the University of Oxford has been used in mobile laboratories capable of running rapid tests in remote locations and even identifying new variants.
The revolutionary CRISPR gene editing technique also makes it possible to diagnose a contagion in 40 minutes . Just a few days ago, scientists at the state center for genomic analysis in New Delhi, India, announced in The Lancet a new diagnostic method that uses CRISPR and that allows detecting a contagion and the variant of interest in an hour and a half and for a price of about 10 euros.
A system developed by Juan Carlos Izpisua's team makes it possible to diagnose a contagion and identify the variant in less than four hours
The advantage of the Izpisua prototype is that it would also be able to detect other viruses whose symptoms could be confused with covid, such as influenza and other coronaviruses other than SARS-CoV-2. "The sensitivity is comparable to current PCR assays," explains Izpisua. "The estimated false negative rate is 3.8% and the estimated precision for the detection of SARS-CoV-2 is 93%," he adds. The Universidad Católica San Antonio de Murcia has also participated in this research.
“In developed countries like Spain, PCR is not a problem, there would be no need to replace it with systems like this one”, explains Carmen Cámara, spokesperson for the Spanish Society of Immunology. “But this type of instrument would allow a much more complete follow-up of the variants than the current one and much faster, which is very important. Here in Spain we have to do a much better follow-up than we do ”, he highlights. "In addition, these types of devices can be essential in the third world, where there is no abundance of PCR," he adds.
The European Union recommends that countries sequence the genome of at least 10% of all cases detected by PCR, a goal that Spain is still far from and that is only surpassed by countries such as the United Kingdom or Denmark, which are making a special effort of sequencing.
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"Due to the drop in cases nationwide, we should now be sequencing about 5% of all positive cases", explains Iñaki Comas, co-director of the Spanish consortium that monitors the coronavirus genomes. Comas highlights that despite the decline in infections Spain is "at a very dangerous time." “Epidemiological surveillance of new variants is more important than ever. We still have a large part of the population that is not vaccinated and that reduces the selective pressure on the virus and can give it scope to find new solutions, for example mutations that allow it to escape vaccines ", he highlights.
" This type of devices is a step forward in the application of massive sequencing techniques in the diagnosis and characterization of pathogens ”, says Fernando González Candelas, co-director of the Spanish sequencing consortium and geneticist at the University of Valencia. "It will work better with viruses, but it could also spread to bacteria, with some modifications," he highlights.
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