Tuesday 7 February 2023

Omicron is present throughout Costa Rica; becomes the most common

Genomic analysis indicates that 47 of the 88 cases studied in the last analysis correspond to this variant; there are 65 reported cases

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QCOSTARICA – The omicron variant of SARS-CoV-2, the virus that causes covid-19, is already present throughout Costa Rica. In a matter of two weeks, this became the most common in the samples analyzed by Costa Rican scientists, as it was detected in 47 of 88 cases (53.41%) studied. The remaining samples correspond to the delta variant.

Genomic surveillance is carried out to determine the presence of the different variants of the SARS-CoV-2 virus in the country.

The team, led by the Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), – Costa Rican Institute for Research and Teaching in Nutrition and Health, assured that with these new samples 65 cases of this variant are already confirmed in the country.

It should be considered that less than 1% of patients are tested for the virus.

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The affected people are between the ages of 9 and 75; There are 33 women and 14 men. Only one has required hospitalization. The others report joint and muscle pain, headache, sore throat, fever, cough, nasal congestion, and rhinorrhea (runny nose).

Of the 47 new cases, 40 are Costa Rican and seven are foreigners. Of the nationals, nine indicated having recently traveled to different countries, among which the United States, Colombia and Israel stand out.

Where are the people already confirmed as omicron from? The new cases correspond to six provinces.

  • San José: central canton, Aserrí, Desamparados, Escazú, Goicoechea, Montes de Oca, Puriscal and Santa Ana.
  • Alajuela: Central canton, San Carlos, Río Cuarto and Grecia.
  • Heredia: Central canton, Barva and Santo Domingo.
  • Puntarenas: Central canton, Garabito, Quepos and Coto Brus.
  • Cartago: Central canton, Paraíso and Oreamuno.
  • Limon: Talamanca.

Guanacaste did not report cases in the last analysis, but in the one released on December 28, they had already been reported in La Cruz and Liberia.

How is Omicron ‘searched’ for?

In a previous interview with La Nacion, the microbiologist Hebleen Brenes, in charge of the SARS-CoV-2 event at the Reference Center for Incense Virology (a laboratory that sees all respiratory viruses) and Francisco Duarte, director of the Genomics Laboratory of that same institution, explained how an active search for the different variants of concern (VOC) is carried out.

Genomic surveillance begins as soon as people go to public and private laboratories for a diagnostic test. A percentage of the tests that are positive are sent to Inciensa for analysis. Before the omicron announcement, this surveillance has intensified.

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There are samples that are taken as a priority for these investigations. Among them are:

  • People entering the country. This includes tourists and nationals and residents who were outside the country and manifest symptoms in the first 14 days after entering the country. This is important to “fence” possible infected cases abroad and import the variant.
  • Foci or clusters of infection in specific areas. Brenes explains that, as omicron is so potentially transmissible, an unusual increase in cases related to each other or in a certain area could be a sign of the appearance of the variant.
  • People vaccinated or reinfected. Some of the mutations contained in omicron suggest that they might escape the protection generated by natural infection or by vaccines. Therefore, attention is paid to this type of case, since it is more likely that it is an omicron.

However, Inciensa receives other types of positive samples that do not fall within this prioritization in order to have the greatest possible variety.

The first thing that is done with the samples obtained from the laboratory is to see, through a PCR analysis, if any of them have any genetic characteristics that differentiate them from delta, and that they indicate that it may be omicron. The Virology Reference Center is in charge of this process.

Those samples that are filtered by screening and present some omicron-specific characteristics should undergo a more in-depth analysis to confirm or rule out that they really are.

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If it is determined that a sample has some omicron-compatible characteristics, the final step is performed. At the Genomics Laboratory, a gene-by-gene analysis of the virus is carried out.

Read more at La Nacion.

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