Science in Costa Rica is scanning the coronavirus for mutations and variants
The presence of the delta 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, it was found that they had this terrifying 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 Education in Nutrition and Health (Inciensa) with support from the University of Costa Rica (UCR) and Children’s National Hospital (HNN).
How is this process? his mom Talk to Francisco Duarte, director of the Incense Genome Laboratory, for more details.
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 accurate analysis began, months after the start of the approach that allowed us to begin to detect.
The genome indicates the complete “fingerprint” of the virus in detail. Based on this information, better decisions can be made to deal with this.
According to Duarte, this process consists of two parts, the first of a laboratory nature and the second of bioinformatics.
The first starts when 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 universal tests.
Right now, this step has a component that hasn’t been around for a few months and is accelerating: there are already specific tests that detect specific variants and inform you when a full genetic analysis is done.
These detailed tests “look” for three variables of concern (VOC), which, due to their transmission or behavioral characteristics, have been closely followed: alpha (first seen in the UK), beta (seen in South Africa) and range (a remarkable feat) discovered in Brazil).
This way, whenever you have samples, you must first pass 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.
So is the delta: anything negative in these specific tests is subject to a full-genome screening. Then this analysis found the mutations that characterized the delta.
Likewise, it was determined in the analyzes that the so-called “ethical alternative” had almost completely disappeared.
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 authentic, so it was easy for a different kind of our country to emerge, opening up more VOCs, more infections, which became more prevalent.”
Better knowledge of the virus and technology, as well as more resources, allowed us to move forward.
At the beginning of the epidemic, in April of last year, the first six complete genomes were accessed, then 24 and then 48 were made. 2020 ended with about 200 analyzes.
So far in 2021, 600 tests have been conducted.
“In less time we will have three times the genome.
“We start by testing different protocols in labs, different techniques, and different reagents to see which one gives the best results, and in this case, it’s not like it ‘matches’ the protocol,” he said.
Later, as the disease progressed, he gave advice on how to proceed.
The expert 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 talking about the racetrack in Brazil.
Another candidate was unexpected outbreaks in certain areas or strange displays of disease.
Now, with more specific testing for VOCs, this simplifies further investigations into the delta variant or others that may arise in the future.
For now, 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 people, and people with immune problems and infections.
This will give you a better idea of the virus that is spreading in our country.
Currently, 100 to 200 genomes are generated per month for cases detected across the country. Additional features should be up to 500 per month.
For the future
The scientist understands that Costa Rica cannot meet the goal of some organisms of sequencing the genomes of 1% of cases. This idea was born in European society, in countries with completely different characteristics from ours.
“We will not compare the production capacity of Costa Rica with the capacity of the United Kingdom, which has access to this part,” he said.
Therefore, he notes that not all functions can be used to “track” deltas, but also other variables of concern that may arise.
like a book
For Alan Orozco, director of the Central American Bioinformatics Network, checking for a virus is like translating a book into an unknown language.
This book consists of 30,000 letters that identify your genetic material. Each page consists of the following set of letters: A, C, G, U. We should translate and read this book to discover the genome,” the bioinformatics scientist said in an interview a few weeks ago.
Each time the virus replicates, it changes, such as when multiple copies of previous copies are made and the leaf does not look the same.
It is these changes that will define the variables.