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Covid-19: Study points to new answers on the onset of community transmission


Lucas Rocha (IOC/Fiocruz)


With the goal of better understanding the beginning of the novel coronavirus pandemic in Brazil, researchers of the Oswaldo Cruz Foundation (Fiocruz) have carried out a wide genetic study involving almost a hundred samples from patients from all Brazilian regions, infected by the SARS-CoV-2 virus in the early moments of the pandemic in national territory.

The study was led by specialists of the Respiratory Viruses and Measles Laboratory, national reference for respiratory viruses for the Ministry of Health and a World Health Organization (WHO) reference for Covid-19 in the Americans, as well as of the Aids and Molecular Immunology Laboratory of the Oswaldo Cruz Institute (IOC/Fiocruz). The research also counted on the participation of professionals of the General Coordination of Public Health Laboratories of the Ministry of Health, of the Evandro Chagas Institute (IEC), of the Federal University of the state of Espírito Santo (UFES), of the Federal University of the state of Mato Grosso do Sul (UFMS), of the University of the Republic of Uruguay, of Public Health Central Laboratories, and of the Fiocruz units in the states of Bahia and Mato Grosso do Sul.

According to the leader of the study, researcher Paola Cristina Resende, of the Respiratory Viruses and Measles Laboratory of IOC/Fiocruz, sequencing the full viral genome is an important tool for the knowledge on virus dissemination, in Brazil as well as in other countries. “The characterization of viral lineages allows us to understand the type of virus that is circulating in a certain region and to make comparisons with the circulation of lineages between countries and even within the same country. It is an important step to comprehend how the lineage is behaving and dispersing in each geographical region”, she explains.

To get to the results, the researchers sequenced samples obtained from 95 subjects, collected between February 29 and April 28, from all Brazilian regions, including the Federal District, and nine states: Rio de Janeiro, Espírito Santo, Acre, Amapá, Pará, Alagoas, Bahia, Maranhão, and Santa Catarina.

Based on the analysis, specialists detected six lineages of SARS-CoV-2 circulating in the country (A.2, B.1, B.1.1, B.2.1, B.2.2, and B.6). Most sequences obtained in the study were classified as clade B.1, with a predominance of sub-clade B.1.1. According to Paola, the prevalence of sub-clade B.1.1 in the samples was even higher when compared with other Brazilian sequences available on GISAID, an international genomic database of influenza viruses and of the novel coronavirus. “Clade B.1.1 was the only lineage detected in individuals without a recent history of international travels, while four different lineages were detected among the six individuals who had recently been abroad, that is, imported cases, and their contacts”, she highlighted.

To investigate the high prevalence of the lineage, researchers made a phylogenetic analysis, a sort of viral family tree. The 95 Brazilian sequences were compared with 3,764 other sequences available on GISAID. The investigation counted on the participation of researcher Gonzalo José Bello Bentancor, of the IOC Aids and Molecular Immunology Laboratory. The results suggest that the lineage first appeared in Europe around February 2, and got to Brazil a few weeks later, originating from multiple independent introductions. The analysis show that the lineage reached different regions of the country in mid March. The study also shows that the lineage was found in neighboring countries in South America, such as Argentina, Chile, and Uruguay, and in more distant countries too, such as the United States, Canada, the United Kingdom, and Australia.

The initial characterization of the lineage pointed to two amino acid replacements in the structure of the virus. Due to these small mutations, researchers named the lineage B.1.1.BR. Additional studies will be necessary to show possible implications of this mutation in factors such as transmissibility or impact of the infection, for instance.

Read more: 

Fiocruz develops a protocol to sequence the new coronavirus

Study identifies different lineages of the novel coronavirus in the Amazonas state

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