Brazil is experiencing one of the worst moments of the pandemic, with a growing number of infections and deaths due to covid-19.

The spike in cases in recent days has been attributed in part to the spread of a highly contagious variant of the virus, called P.1, which is believed to have originated in the Amazon city of Manaus.

Experts warn that what is happening in Brazil is just one example of the importance of tracking the emergence of variants of the SARS-CoV-2 virus in Latin America.

This trace is known as genomic surveillance, and, according to the experts consulted by BBC Mundo, it is a task in which Latin America is lagging behind.

Specialists agree that, although there has been progress, in the region it is necessary to strengthen genomic surveillance and warn about the risk not to do it on a large scale.

“Latin America needs strong genomic surveillance. In most countries it is still minimal,” epidemiologist Zulma Cucunubá, a specialist in infectious diseases and public health at Imperial College London, wrote on Twitter in early March.

“We do not know what is happening with the SARS-CoV-2 variants in the region.”

What is genomic surveillance and what is its status in Latin America?

The genetics of the virus

Each SARS-CoV-2 virus has a genetic code that is expressed in a sequence of 30,000 letters.

This set of letters is known as the virus genome, and is the one that gives you the instructions to function and transmit.

Also, those letters function as a “historical archive of the evolution of the virus“, as Fernando González Candelas, professor of genetics at the University of Valencia, in Spain, explains in an article published in The Conversation.

Every time the virus infects a new person, there is a chance that mute, a characteristic of viruses.

Thus, scientists can tell that a virus mutated by noticing that some of the letters in its genome changed.

Mutations happen all the time, but when a group of viruses share the same set of mutations they form what is known as a variant.

Variants of SARS-CoV-2 have been identified in various parts of the world during the pandemic.

Some of them are what are technically known as “variants of concern”, because they have the potential to be more contagious, cause more serious illness, or reduce the effect of vaccines.

So far, at least three variants of concern have been identified:

  • B.1.1.7, first identified in the UK
  • B.1.351, first identified in South Africa
  • P.1, identified for the first time in Brazil

“The virus is not a static unit but it is changing,” Julián Villabona, molecular epidemiologist at the Center for mathematical modeling of infectious diseases at the London School of Hygiene and Tropical Medicine, tells BBC Mundo.

“If given the opportunity, it will change in ways that allow it infect more people or in some cases cause a more serious illness. “

  • 4 findings and 3 unknowns about the origin of the coronavirus left by the WHO report

Track the variants

These variants have been identified thanks to the fact that scientists share thousands of virus genomes in a large global database.

This database is called GISAID (acronym for Global Initiative on Sharing All Influenza Data, Global Initiative to Share All Influenza Data, in Spanish).

Its name is due to the fact that it was originally created to monitor the genome of the virus of the influenza.

What researchers do at GISAID is deposit the 30,000 letters of the virus that infected each person they manage to register.

In the pandemic so far, experts have learned that SARS-CoV-2 accumulates one to two mutations per month, as Villabona explains.

Thus, genomic surveillance must review the 30,000 letters of the virus that infects each person and observe what changes have occurred with respect to other people’s viruses.

“Genomics is the only technology that allows us to identify the new variants that concern us, “Catalina López Correa, a medical specialist in genetics and executive director of the Canadian Covid-19 Genomics Network (CanCOGeN), tells BBC Mundo.

“If we do not understand what variants we have and how they are being transmitted, we have the risk that at some point the vaccines are not effective“.

For his part, Villabona adds that “genomic surveillance allows us to be aware that the virus does not change in ways that complicate the situation, and that if it is changing, strategies can be activated to reduce the impact. “

The equation is clear: the greater the number of variants, the number of infections may increase; and the greater the number of infections, the greater the probability that new variants will appear.

Surveillance in Latin America

Genomic surveillance of SARS-CoV-2 in Latin America “is in an embryonic state”, in the words of López Correa.

The expert comments that the United Kingdom, for example, has registered about 300,000 genomes of the virus in GISAID. Canada has registered more than 22,000.

As of March 22, Latin America and the Caribbean, as a whole, had registered less than 14,000, according to the Regional Network for Genomic Surveillance of covid-19, which has the support of the Pan American Health Organization (PAHO).

As of March 31, GISAID had more than 940,000 sequences of SARS-CoV-2 on its platform globally.

López Correa highlights that, in Latin America, countries such as Mexico and Brazil lead the number of recorded sequences, and that in Colombia, Peru and Ecuador the number of reported genomes is increasing little by little.

The expert, however, warns that “come on slow“.

“I think that in Latin America we are not being very conscious how important genomic surveillance is. “

For his part, Villabona maintains that the number of genomes reported from Latin America is very low compared to the total number of covid-19 cases in the region, which is around the 24 millions contagion.

“In Latin America there is the possibility that variants that have not been reported and that they are responsible for a significant fraction of the cases, “says Villabona.

“That cannot be known, because there is no genetic data … with that number of sequences that we have it cannot be calculated. “

At a press conference on March 23, PAHO said it is supporting Latin American countries to strengthen their virus surveillance capacity, and that one of its main objectives is to expand that tracking network with new laboratories, funds and technical assistance.

Priority

Experts agree that Latin America has people trained to do more genomic surveillance.

López Correa, however, maintains that “there is a lack of resources and to give priority to it from a strategic and political “.

The expert indicates that genomic surveillance is an important tool for making public health decisions such as confinements, for example.

“At this time vaccination and surveillance they are equally important, “he says.

For his part, Villabona maintains that so far Latin America has focused on monitoring whether there is a presence of a variant from another region, but that a greater effort should be made to know if a variant of own continent it has the same effect.

In Brazil, for example, it was important that a few years ago a genomic surveillance program for viruses such as that of the dengue, Zika or yellow fever.

As Villabona explains, thanks to the fact that this infrastructure already existed, it could be adapted to track the coronavirus genome.

Finally, although experts insist that the governments of each country prioritize genomic sequencing at the national level, the issue of surveillance should be seen as a matter of cooperation global.

If a country does not adequately monitor the possible variants, it can become a public health problem at a global level.

“For the virus there are no borders”, concludes López Correa.

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