Covid-19: Fiocruz Genomics Network will sequence the virus samples in Brazil

The Fiocruz Genomic Network is participating in a project by the Ministry of Health that will sequence new coronavirus samples throughout the national territory. Currently, only three central laboratories (Lacens) in the states are capable of this task. The Network brings together researchers from various institutes of the Foundation to study genetics and genomes of viruses, bacteria, fungi, parasites, and humans, in addition to receiving support from the Network of Technological Platforms (in Portuguese, Rede de Plataformas Tecnológicas), with access to sequencers and bioinformatics.

During the pandemic caused by the new coronavirus, a main focus of the group has been the Sars-CoV-2 genome study, which causes Covid-19, and its genetic mutations monitoring, among others. The group participates in the Global Initiative on Sharing All Influenza Data, GISAID, which produced the infographic of Sars-CoV-2 strains circulating in the world. “At the moment, all of our attention, in the case of the genome platform, is focused on the coronavirus, due to the pandemic urgency, but the Network also operates on other fronts, which was what led to its creation, aiming at these researches integration”, stresses the vice president of Research and Biological Collections, Rodrigo Correa de Oliveira.

Fiocruz President, Nísia Trindade Lima says that a Genomic Network will integrate a collaborative process with surveillance systems across the country, grouping the operating data to identify the coronavirus new variants and strains. Vice President Rodrigo Oliveira adds that the Foundation will be responsible for sequencing in several states and for curating sequencing, within a very broad program, which brings together all of Fiocruz.

According to him, almost all Fiocruz units have sequencers and those that do not have, will have it as soon as it is possible to acquire. “Our differential is that we cover a very large territory, we have a fully integrated network and we also provide external services, to universities and other institutions”, says Oliveira. The Research Vice Presidency coordinates the Genomic Network, which brings together other platforms, such as microscopy and proteomics, in a total of 13.

For this challenge of mapping the entire Brazilian territory, Fiocruz offers a great asset and occupies a central role, since it has laboratories with sequencing capacity in several states. "With the Ministry of Health support, we will be able to fulfill this mission and do our work in a very detailed way". Oliveira said that the Foundation has also collaborated with countries in Latin America in this field, through the Pan-American Health Organization (PAHO).

Sequencing

The sequencing project will be carried out in the states, with the sending of some samples to the laboratories, such as those from Minas Gerais and Paraná. In other cases, such as Rondônia and Ceará, investments are expected to increase the sequencing capacity. “The group that discusses this project drew up how it will be done by regions, to be as representative of the national reality as possible, and is led by researcher Marilda Siqueira, head of the Laboratory for Respiratory Viruses and Measles at the Oswaldo Cruz Institute (IOC/Fiocruz)”, points out Oliveira, who at Fiocruz is in charge of this project, together with the coordinator of Health Surveillance and Reference Laboratories, Rivaldo Venâncio.

According to Venâncio, “the epidemiological situation that Brazil is experiencing in this pandemic requires continuous monitoring by all health institutions, in order to detect possible new situations that require a quick intervention by the public authorities”. Among these actions, he adds, is the need to broaden the Sars-CoV-2 variants emergence monitoring.

One of the coronaviruses characteristics is the high capacity to produce mutations in their genetic structures. “As a result, we need to monitor the new variants emergence trying to correlate them with Covid-19's epidemiological dynamics. In other words, is the appearance and spread of variants having an implication from the clinical point of view? Are people having more serious cases? Or not? These are the questions we are going to ask. On a larger horizon, we are also concerned with the vaccines protection”.

Venâncio stresses that this is a very daring project. “They are not just answers for this moment, but for the coming months and years. We will monitor any and all genomic variations of the virus that are detected anywhere in the country and correlate this appearance with epidemiological and clinical aspects ”.

For the Health Surveillance and Reference Laboratories coordinator, “it is possible to foresee that the pandemic can be overcome with the expansion of mass vaccination, but most likely Covid-19 will continue to exist, although on a smaller scale. We have to observe the virus and the disease, the severity, and the behavior of the genetic variation in relation to the vaccines that will be used. These studies will contribute decisively to generate scientific evidence on the need to update or not the vaccine content in the coming years ”.

Exclusive data

Vice President Rodrigo Oliveira notes that the Fiocruz Genomics Network, which began to be thought of in March 2020 and was finally formatted in October, is one of this process spearheads at the institution. The Network brings together about 100 researchers from different Fiocruz units who work with genetics and genomes of viruses, bacteria, fungi and parasites, and humans. The Network has been working to optimize and standardize the entire sequencing process, establishing unique protocols for all laboratories in the network.

Focusing on the Brazilian situation, the Fiocruz Genomic Network started to make exclusive data on the country available on the initiative's website. “For the rapid progress in understanding Covid-19 and its complications, it is essential to strengthening scientific collaboration. Through genomic data, it is possible to advance in research and development of possible vaccines and drugs, in addition to keeping the diagnostic kits always up to date with the circulating genomes and the surveillance of virus dispersion always alert, even more at a time when it is being observed the new coronavirus variants emergence", emphasizes researcher Marilda Siqueira. She heads the Laboratory of Respiratory Viruses and Measles of the Oswaldo Cruz Institute (IOC/Fiocruz), which is a National Reference Center for respiratory viruses for the Ministry of Health and a reference for the World Health Organization in Covid-19 in the Americas.

According to the data available on the Fiocruz Genomics Network website, approximately 3,600 sequences of the Sars-CoV-2 genome have already been carried out in Brazil, with São Paulo being the state with the largest number of sequenced samples, with a total 1,035, followed by Rio de Janeiro, with 726, Amazonas, 340, Rio Grande do Sul, 306, Paraíba, 167, and Pernambuco, with 150.

According to the initiative, more than 60 new coronavirus strains have already been identified in the country. However, experts highlight the predominance of lines B.1.1.33 and B.1.1.28, which have had national circulation since March 2020. The line B.1.1.28 gave rise to two lines that started to circulate more recently in the country, P.1 and P.2, scientifically called variant of concern (VOC).

In relation to Amazonas, which faces serious problems in its health system, the data indicate the accelerated advance of the P.1 strain, discovered in the state. The recent variant, derived from one of the lineages that predominated in the country, B.1.1.28, is currently responsible for more than 91% of infections in the state. Studies indicate that the variant contains at least three mutations (K417N, E484K and N501Y), which affect the protein Spike, associated with the entry of the virus into human cells. P.1 was also identified in 16 other states, São Paulo, Goiás, Paraíba, Pará, Bahia, Rio Grande do Sul, Roraima, Minas Gerais, Paraná, Sergipe, Rio de Janeiro, Santa Catarina, Ceará, Alagoas, Pernambuco e Piauí.

“In order to detect this strain circulation among the population of Amazonas and other states, we are receiving 30 to 40 positive samples from different locations to perform the sequencing and understand the possible dispersion of this and other strains”, explains virologist Fernando Motta, researcher at the Laboratory of Respiratory Viruses and Measles at IOC/ Fiocruz. “Studies are being conducted with samples isolated from different strains in order to identify how the newly described mutations may or may not affect the response induced by the vaccines in use”, adds Motta.