According to the expert, the next step focuses on deciphering the composition of nucleotides that this strand has, since it is what will allow to determine the different variants and observe if there are mutations that condition transmissibility or constitute a threat to the effectiveness of the vaccines, a phenomenon known as immune escape.
The activity consists of two parts: the wet and the dry. The first contemplates several technical steps, while the second is based on the analysis and interpretation of all the data. “When we have selected the samples that we are going to sequence, which is done taking into account the patient's viral load, among other epidemiological considerations, we extract the genetic material and proceed to amplify the genome of the virus divided into multiple fragments. Then, we put some codes that will allow us to differentiate them and to know which samples they correspond to. This is how bookstores are made up », details the professional. Thanks to this technique, 237 regions of the virus are sequenced to cover 99% of the genome. It should be noted that the technical part can take two or three days of work and that another two are needed to analyze and interpret the results.
The truth is that there are a series of mutations that define each variant and that they have to be present to know which one it is. "We have to confirm that the samples have these mutations in order to give them a surname," says the professional.
The British variant is present in 90% of the cases examined by the center since March
But the process is complex, since you have to find out which ones may have epidemiological implications. “All information is shared on a worldwide network so that it can be studied and we have programs to detect patterns, build the structure of the virus protein and locate mutations in it. In SARS-CoV-2, we look at the S gene, where the Spike protein is found, which is the one involved in the binding of the virus with cells. In this way, we can know if it can condition transmissibility, because the pathogen binds better, or if there may be a potential immune escape, "he says.
What are the most worrying strains? According to the microbiologist, this is something determined by the European Center for Disease Prevention and Control (ECDC) and information on these is constantly updated. “Right now there are four: the British, the Brazilian, the South African and the Hindu. These are the most important because there is evidence that they may be more transmissible or escape immunity. This is changing and, from one day to the next, a variant can go from being of interest to being worrisome, depending on how it evolves ”, he emphasizes. Also, the Ministry of Health has asked the professionals of the hospitals that carry out mass sequencing to monitor the behavior of certain variants to prevent the epidemiological conflict from worsening.
The results obtained so far have shown that in the north of Gran Canaria, as in the rest of the Archipelago and the national territory, the strain that circulates predominantly is the British one, since it represents 90% of the cases studied. . In fact, there have been times when this percentage has been exceeded.
In this sense, one of the doubts that arises among the population is to understand why some variants prevail over others. “Every time the genetic material of a virus or bacterium is copied, errors will occur. In most cases, they do not cause effects, but in others, these changes can be beneficial and represent an evolutionary advantage over other lineages, ”the physician warns. Although he points out that in other cases the opposite may happen and, therefore, be harmful to the microorganism.
Regarding the repercussions that the new strains may have on the good effects that vaccines have shown, Chamizo emphasizes that this is a matter that must be analyzed variant by variant. "There are mutations that, in in vitro studies, can potentially reduce the neutralization capacity of the vaccine, but it is essential to observe this effect in real life", he adds. This information is published on the ECDC website.
"We believe that the incorporation of this technology is something very positive", indicates Chamizo
For the Microbiology Service of the northern hospital, starting the career of the massive sequencing of SARS-CoV-2 has been a challenge. The center had no experience in this new generation of the technique, but it applies the Sanger method - older, but very precise - to detect the mutations that lead to the development of resistance to antiretrovirals intended to treat HIV infection. Now, the purpose is to extrapolate the new generation to other fields. “We believe that the incorporation of this technology is something very positive for the hospital and that is why we are fighting to implement it. Years ago, I was trained in sequencing targeting bacteria, but the rationale behind the technique is the same, ”says the specialist.
In fact, one of the advantages of also using it to study bacteria is that it could detect outbreaks in the hospital. "We think that this activity will end up being carried out in most of the Microbiology services and, probably, within a few years it will represent an advance in the diagnosis of infections that right now can constitute a challenge, such as those caused by non-culturable microorganisms", he adds Chamizo.
The objective is to extrapolate the new generation of technology to other fields
In his opinion, sequencing the coronavirus is an essential task to undertake control measures before a variant is installed in a specific geographical area and, subsequently, spreads to other countries. “Governments have recommended this practice, precisely, to prevent this from happening. If variants of interest or problems are identified that are not yet circulating in Spain, for example, when they arrive, we can try to locate the index patient and take the necessary measures to try to contain the dispersion in that area ”, says the microbiologist.
It should be remembered that, since January of this year, the European Commission recommended nations to sequence between 5 and 10% of positive samples from patients. That same month, the Ministry of Health of the Government of Spain approved the Protocol for the Integration of Genomic Sequencing in the Surveillance of SARS-CoV-2, which includes a document prepared by the Alerts Report, in collaboration with the Carlos Health Institute. III. Through it, a guide is offered to identify new variants and their incidence.
An essential task
The University Hospital of Gran Canaria Doctor Negrín began to carry out the massive sequencing of SARS-CoV-2 since last March and, at the end of that month, it obtained the first results. «A few years ago I received training at the University Hospital of La Paz, but focused on the sequencing of bacteria. The coronavirus pandemic has now made it necessary to apply the technique to analyze virus mutations, "explains Francisco Javier Chamizo, in charge of carrying out this task at the reference health center in the northern area of Gran Canaria, together with the technician responsible for the Sequencing area, Nereida González. YM