Study shows eight lineages of the new coronavirus in the Amazonas state

Nine months after the appearance of the first case of Covid-19 in the state of Amazonas, researchers of the Leônidas & Maria Deane Institute (ILMD/Fiocruz Amazonia) have already sequenced 79 genomes of the Sars-CoV-2, using samples obtained from 18 of the state’s municipalities. The research is a partnership with the Health Surveillance Foundation of Amazonas (FVS/AM), by means of the Central Laboratory of Public Health (Lacen-AM), within a strategy of surveillance for emerging/reemerging and neglected viruses, which started 5 years ago.

Captained by researcher and vice-president of Research and Innovation of ILMD/Fiocruz Amazonia, Felipe Naveca, the study has found eight lineages of the new coronavirus circulating in the state, suggesting at least eight introductions of the Sars-CoV-2 in the Amazonas state. Another relevant discovery was the identification of four lineages that had not been sequenced in Brazil so far.

The four new identified lineages are B.1.107; B.1.111; B.1.1.2; and B.1.35, which circulated in Denmark, Colombia, the United Kingdom, and Wales, respectively. This makes the number of lineages found in Brazil jump to 30.

“The more we investigate, the more variability we find, proof that the virus has entered the state on several occasions, even during a period in which people circulation was reduced - at least in theory.

The samples sequenced in ILMD/Fiocruz Amazonia come from the municipalities of Anori, Autazes, Careiro, Iranduba, Itacoatiara, Jutaí, Lábrea, Manacapuru, Manaquiri, Manicoré, Maués, Nova Olinda do Norte, Parintins, Presidente Figueiredo, Santa Isabel do Rio Negro, Santo Antônio do Içá, and Tabatinga, in addition to the state capital, Manaus.

The researcher emphasizes the importance of sequencing the new coronavirus and to give continuity to this work, including diagnostic protocols. “The data provided by the sequencing also help us verify whether it is necessary to make adjustments to diagnostic protocols - for instance, if the virus has accumulated mutations here that lead to false-negative results. The protocols used today were developed in other countries, such as China, USA, and Germany, taking into account what was known of viral variability at that moment in time”, he states.

For Cristiano Fernandes, technical director of FVS-AM, new issues arise as the lineages of Sars-CoV-2 circulating in the Amazonas state are identified, especially regarding the itinerary of the virus until it was introduced in the municipalities. “Our challenge is to expand the samples from municipalities in the hinterland to attempt to identify higher viral variability, understanding the context and the complexity the disease has brought us. We must keep in mind that there have been almost 4,600 deaths in this state, so there are still questions waiting to be answered, and this study can clarify much in terms of surveillance, this aspect related to the pathology of the disease, based on genomic studies and viral variability studies”, Fernandes says.

Genomics in Amazonas 

In March this year, a few days after the occurrence of the first case of Covid-19 in the state of Amazonas, Felipe Naveca concluded the first sequencing of the genome of Sars-CoV-2 in the northern region of the country. The study is continuous, given the importance of a better understanding of virus dispersion in the Amazonas state. Sequencing the genomes of SARS-CoV-2 samples helps develop vaccines and drugs against the virus. The genomes identified in Amazonas are part of a database and can now be compared to others circulating in Brazil and abroad.

The study by Felipe Naveca and his team is supported by the Foundation of Support to Research of the State of Amazonas (Fapeam) and by Fiocruz.