The University of Guadalajara (UdeG) and the biotechnology innovation company Genes2Life, which work to detect covid-19 mutations in residents of Jalisco, found four cases of the mutation E484K virus on January 27, the first being found in Puerto Vallarta, which is 50% more contagious than the original strain.
The E484k mutation means that the virus is less detectable by the immune system, there is a delayed response to infection, and it is more contagious.
The academic collaboration between the University and the company that is also dedicated to molecular biology diagnosis began in January, says Francisco Muñoz Valle, rector of the University Center for Health Sciences (CUCS) at UdeG.
“We started to design a method to look for two mutations that have been described as the most important, N501Y and E484K. In 700 samples that were taken in December and until January 15, we have not found the N501Y mutation, which also belongs to the British strain and the South African strain”.
“But in our population, we identified four people with the E484K mutation, this mutation belongs directly to the South African and Brazilian-Japanese strain. However, it does not mean that with this mutation we have identified a new strain or a new lineage”.
He indicated that the identification of E484K in the four patients is relevant because it is an escape mutation. This means that “those patients who can be infected with this strain, or who have a SARS-Cov2 with this mutation, the antibodies generated by having had a primary infection or those patients who have been vaccinated, possibly there is a reduction in the binding of antibodies to the virus, and it is more difficult to eliminate it”.
He specified that to know if it is a new strain or lineage, it is necessary to sequence the four samples.
“We identified a mutation that is found within the South African strain or the British or Japanese strain, but we have not defined that we have the other mutations in these four samples from the Jalisco population, for this we have to sequence, that’s why we started in contact with the State Secretariat of Health and with the National Institute for Epidemiological Diagnosis and Reference (InDRE), which is the governing body to be able to define and sequence it,” he explained.
He explained that genomic sequencing will take three to four weeks, due to the lack of the necessary infrastructure, and the molecular methodology “is not easy; precisely for this reason we designed a method to search in a targeted way for these two mutations in positive samples from the population”.
Of the four patients between the ages of 30 and 60, who live in the metropolitan area of Guadalajara, and who traveled to Puerto Vallarta where they were infected, said that they were tested for COVID-19 in December, they did not present serious symptoms and they have come out of their infection.
With the research, it would be evaluated whether any person who has already been infected would present more severe symptoms in the event of reinfection with E484K and, if they were vaccinated, its effectiveness. “Most of the vaccines were designed to generate antibodies against this region, which is precisely where this mutation is found,” he said.
Muñoz Valle regretted that there is not a large budget to verify if all the tests that are positive for covid-19 present some type of mutation.
“We are doing the analysis with our own resources from the University of Guadalajara and the company, without a direct objective of being able to obtain profits. This is an investigation that we are doing with our own resources (…) and when we have more, we can do it in all the positives that we find directly in our laboratories”, he commented.
UdeG has 10 molecular biology laboratories where 800 to 1,000 daily PCR tests are applied free of charge through the Radar Jalisco program, to which the state government also contributes resources.
The rector of the CUCS also mentioned that he already showed interest in joining the analysis of positive tests for covid-19, in the search for mutations, the State Council of Science and Technology in the state, and the objective would be to examine all samples.
“The goal in an ideal state, I think it would be (to examine) all those positives that we find in the laboratories, at the same time, we could carry out the identification of the E484K mutation in a second moment. However, that will depend on resources”, he pointed out.
The former general director of the Hospital Civil de Guadalajara, and infectologist, Héctor Raúl Pérez Gómez, explained that the E484K mutation is 50% more contagious than the original strain, that of Wuhan, but with similar symptoms.
“This small protein on the surface of this SARS-Cov2 virus is the one that binds to a receptor in the cell it infects and it has been found that strains containing this mutation can be transmitted more efficiently among the population,” he added.
Preliminary studies published in January 2021 report that the mutation of the covid-19 virus negatively affects the performance of the vaccine designed against the Wuhan strain.
Pérez Gómez said that they are “preliminary findings of some laboratory studies, not in humans, which are in the process of being confirmed in the world, but in general it is considered that current vaccines continue to provide protection even for the British, South African and Brazilian strains”.
Is the mutation found in Puerto Vallarta a new strain of COVID-19?
Regarding the molecular sequencing of the E484K mutation carried out by UdeG and the company, he said that the process is time-consuming because it requires “shredding all the segments of the viral genome, and that is complex and requires at least a few weeks”.
Furthermore, “because multiple samples have to be analyzed at random to give us an idea of the proportion in which this mutation may be present.”
To find out if it is a new strain, it is necessary to determine if it is an isolated mutation or is part of a series.
If it is found to be part of a group of mutations, it could be established that it is a new strain.
“Meanwhile, it is only about that mutation (E484K), it is not possible to speak of a new strain, of a new variant, if it is another set of mutations different from those reported in the British, Brazilian, and South African strains, there we could already speak of a new variant, but for the moment it is only that mutation”, he clarified.
He also said that an epidemiological contact tracing of the four cases detected in Jalisco with the E484K mutation would have to be carried out, and a series of genomic sequencing studies of the viruses found in them would have to be carried out to determine if it is unique.
He recalled that the British strain has eight mutations in the structure of the spike particle and is up to 70% more contagious than that of Wuhan, and is present in 70 countries.
While the South African variant has nine mutations, one known as N501Y, as well as E484K, and it has already been detected in 31 countries. This complicates the work to end the pandemic, he said.