Science in Costa Rica scans coronavirus for mutations and variants

The presence of the delta type of virus that causes COVID-19 was confirmed in Costa Rica this week.

To verify this, several tests were conducted that carefully studied each gene of 16 people, who eventually turned out to have this scary variant. Coming to this conclusion also involved dozens of professionals in fields such as microbiology, bioinformatics, and virology.

Everything was coordinated by the Genomic Laboratory of the Costa Rican Institute for Research and Teaching in Nutrition and Health (Inciensa) with support from the University of Costa Rica (UCR) and Children’s National Hospital (HNN).

How is this process? Nation Speak with Francisco Duarte, director of the Incense Genome Laboratory, to find out the details.

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What is being analyzed?

Genes can be more complex in some viruses than others. In the case of SARS-CoV-2, the cause of an epidemic disease, a more precise analysis has begun, months into the approach that allowed us to begin to find out.

The genome indicates the entire “fingerprint” of the virus in detail. Based on this information, better decisions can be made to deal with it.

According to Duarte, this process consists of two parts, the first is laboratory in nature, and the second is bioinformatics.

The first starts from the time a sample is taken from a person to diagnose whether they are positive for the virus or not. Of all the positive tests, a small percentage is selected for the universal test.

At the moment, this stage has a component that has not been there for a few months and is speeding it up: there are already specific tests that detect specific variants and provide when a full gene analysis is performed.

These detailed tests “look” for three variables of concern (VOC), which, due to their transmission or behavior characteristics, have been closely followed: alpha (first seen in the UK), beta (seen in South Africa) and range (done discovered in Brazil).

This way, every time you have samples, you must first go through these tests that determine if you belong to one of these VOCs. Thus, it was determined, for example, that alpha and gamma variants became the majority in recent weeks.

And in this way, too, deltas are found: everything that is negative in these specific tests is subject to a complete genome analysis. And so this analysis found the mutations that made deltas distinct.

Likewise, how the so-called “ethical alternative” disappeared almost entirely has been identified from the analyses.

For Duarte, the latter also tells the story of the virus in our country and the dynamics of behaviour.

“Our country has been very closed off to international travel for several months, and everything was original and that’s why it was easy for a different kind of our country to emerge, by opening up more VOCs, more infectious, that became more dominant.”

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progress

Better knowledge of the virus and technology, as well as greater resources, have allowed us to advance.

At the beginning of the epidemic, in April of last year, the first six complete genomes were achieved, then 24 and then 48 were made. 2020 ended with about 200 analyzes.

So far in 2021 there have been 600 analyses.

“In less time we have three times as many genomes.

“We started by testing different protocols in labs, different techniques and different reagents to see which one gives the best results in each case, and it’s not that you ‘marry’ one protocol,” he said.

Later, as the disease progressed, he provided guidance on how to proceed.

The specialist explains that, for example, when the alpha variant was confirmed in the UK, those with a history of travel to that region were analyzed. The same thing happened when I started discussing the range in Brazil.

Another candidate was unexpected outbreaks in certain areas or strange displays of disease.

Now, with more specific tests for VOCs, this simplifies further research on the delta variant or others that may arise in the future.

At the moment, said Christian Perez, a microbiologist at HNN, there are two intentions for genetic monitoring. The first is to obtain a representative sample of country cases.

The other goes to more specific groups like the ones Duarte already mentioned, but can also include infected and vaccinated, those with immune problems and infections.

This will allow to get a better idea of the virus that is spreading in our country.

At this time, 100 to 200 genomes are generated per month for cases detected across the country. More resources are expected to reach 500 per month.

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to the future

The scientist understands that Costa Rica cannot achieve the goal of some organisms in sequencing the genomes of 1% of cases. This idea was born in European society, in countries with very different characteristics from ours.

“We are not going to compare Costa Rica’s production capacity to that of the United Kingdom, which has how to access that share,” he said.

For this reason, he points out that not all resources can be used to “track” delta, but also for other worrisome variables that may arise.

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like a book

For Alan Orozco, director of the Central American Bioinformatics Network, scrutinizing a virus is like translating a book into an unknown language.

This book consists of 30,000 letters identifying his genetic material. Each page consists of the following combination of letters: A, C, G, U. We should translate and read this book to find out the genome,” the bioinformatics scientist said in an interview, weeks ago.

Each time the virus replicates, it changes, such as when several photocopies of previous copies are made and the paper does not look the same.

These changes are what will define the variables.

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