Variants of the new coronavirus are monitored in Mexico with a Genomic surveillance program

Mexico.- The genomic surveillance allows to analyze and understand the patterns in which it evolves SARS-CoV-2, the way its changes affect the evolution of the pandemic and generating important epidemiological data around Covid-19, while facilitating the development of diagnostic protocols and generating information to develop new efficient vaccines to new variations of the virus.

On Mexico, the SARS-CoV-2 Genomic Surveillance Program of the Mexican Consortium for Genomic Surveillance (CoViGenMex) began its activities in February 2021 to learn about the variants of the covid-19 virus in the region. With data up to August 30 of this year, various variants have been identified in Mexico and it has been seen how delta became the dominant lineage in the country.

The detection of lineages in the country

According to the reports of the Genomic Surveillance Program in Mexico, the genome sequences of the SARS-CoV-2 viruses that circulate in the country have been obtained by CoViGenMex and are deposited both in the country’s MexCoV2 database and in the database. Gisaid International Data Center. Once the viral lineages have been identified, they are reported to the Epidemiological Diagnosis and Reference Institute (InDRE).

Based on global genomic surveillance, the sequences of genomes analyzed in Mexico that have one or more similar genetic changes are grouped into lineages. Since the end of 2020, within the lineages “variants have arisen that pose a greater risk to global public health, associated with epidemiological and biological events,” the MexCoV2 database describes in its latest August report.

These lineages and their variants are classified into different groups according to the World Health Organization (WHO) provision: into variants of concern (VOC), variants of interest (VOI) and variants to be monitored (VOM), “these The latter have a lower alert category than VOC and VOI ”. Locally, CoViGenMex describes the variants of national interest (VIN) that may be relevant in the country, but not globally.

Relevant variants

Currently, the WHO characterizes the variants according to the official Pango system (https://n9.cl/b2eal), although there are currently thousands of variants of the virus, those that have some important and relevant change are in greater public light epidemiological.
The WHO classifies until August 30, 2021 as variants of concern the following: alpha (B.1.1.7), beta (B.1.351; B.1.351.2; B.1.351.3), delta (B. 1.617.2; AY.1, AY.2; AY.3; AY.4; AY.5; AY.6; AY.7, AY.8, AY.9, AY.10; AY.11; AY. 12) and gamma (P.1; P.1.1; P.1.2; P.1.4; P.1.6, P.1.7; P.1.8).

Those of interest are eta (B.1.525), iota (B.1.526; B.1.526.2), kappa (B.1.617.1), lambda (C.37) and mu (B.1.621). The variants that must be monitored are B.1.1.318, B.1.1.519, B.1.1.523, B.1.214.2, B.1.427, B.1.429, B.1.466.2, B.1.619, B .1.620, C.36.3, C.36.3.1 and R1.

Variants in Sinaloa

As in all of Mexico, in the northwest of the country the delta lineage grew from May to August, according to Gisaid data. In Sinaloa it was no different, delta (B.1. 617.2) was present in the last month of measurement, in 84.62 percent of the samples, being delta (AY.12) only 7.69 percent of the samples as well as gamma (P.1.2).

The data collected by the CoViGenMex Consortium are important locally and internationally and give a clear idea of ​​the behavior of vaccines, for example, the average age of the samples collected initially was 43.89 years (ranging from 0 to 90 years old) , and in the last two months that age decreased to an average age of 22.89 years, possibly because in the first months of sampling the vaccines were applied in people over 60 years of age, which decreased infections in older ages.

On the other hand, monitoring makes visible the evolution of the pandemic around the presence of the most successful variants, which makes it convenient to continue with this epidemiological work in Mexico and the world.

Sequences present in Mexico

The Gisaid database has analyzed a total of 23 thousand 139 sequences from Mexico, in which the presence of the alpha lineage (B.1.1.7), of English origin, was found in the 32 states of the republic with a number of one thousand 713 sequences; the South African lineage beta (B.1.351) was found in six states with 2,469 sequences detected. Of the delta variant originating in India, 5 thousand 030 sequences were found out of the total, being the delta (B.1.617.2) the most numerous lineage with 2 thousand 469 sequences detected and present in the 32 entities of the republic, it is followed delta (AY.4) with 1,225 sequences and present in 26 states of the country.

Third, Delta (AY.12) was found with 1,184 detections in 31 of the 32 entities. The Brazilian gamma variant (P.1) has been detected among covid-19 patients throughout the country since January 28, 2021, with a total number of 2,332 sequences.

Lineages of interest and monitoring

Among the variants of interest or VOI that were registered in Mexico, the most abundant was mu (B.1.621) with 340 sequences in 25 states. The second most abundant was lambda (C.37), native to Peru, with 197 sequences identified in 18 states; in third place, iota was located, the New York strain with a number of 57 identifications in 14 state locations.

Among the VOM or monitoring variants, only three were registered in Mexico: B.1.1.519, with a very abundant presence of up to 7,784 sequences among the total of the samples, something characteristic only of Mexico; B.1.429, B.1.427 (similar), was registered 485 times in 30 entities, and B.1.1.318 was presented seven times of the total in five Mexican state localities.

To understand …

Genomic Surveillance Consortium

Mexico is part of the Regional Covid-19 Genomic Surveillance Network created in 2020 with the help of the Pan American Health Organization. The work of the Mexican Genomic Surveillance Consortium (CoViGenMex) is to identify mutations that could affect the transmissibility, replication capacity and / or pathogenicity of the virus, that is, the way in which it causes infection, in addition to knowing the existence of mutations that they evade the natural immunity of the human body or that generated by vaccines.

SARS-CoV-2 mutations can also affect the efficacy of molecular diagnostic methods or specific antiviral drugs against the virus that may be designed in the future, therefore it is vital to know the changes of the virus during the pandemic (CoViGenMex and OPS).

The data

Alpha Descent

The alpha variant increased gradually during the year, going from showing 1 percent of the samples in March to 18 percent in May. But it fell to 14 percent in June, remaining at 3 percent in August (CoViGenMex).

Read more: Back to school has not generated a rebound: López-Gatell reports sixth consecutive week with declining covid infections

Delta Increase

At the same time that alpha decreased, gamma and delta increased, but gamma gave way to the rapid growth of delta, becoming the dominant variant in August with more than 91 percent in the Mexican sequences (CoViGenMex).

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