Multiple epicenters of the SARS-CoV-2 pandemic have emerged since the first pneumonia cases in Wuhan, China, such as Italy, USA, and Brazil. Brazil is the third-most affected country worldwide, but genomic sequences of SARS-CoV-2 strains are mostly restricted to states from the Southeast region. Pernambuco state, located in the Northeast region, is the sixth most affected Brazilian state, but very few genomic sequences from the strains circulating in this region are available. We sequenced 101 strains of SARS-CoV-2 from patients presenting Covid-19 symptoms that reside in Pernambuco. Phylogenetic reconstructions revealed that all genomes belong to the B lineage and most of the samples (88%) were classified as lineage B.1.1. We detected multiple viral introductions from abroad (likely from Europe) as well as six local B.1.1 clades composed by Pernambuco only strains. Local clades comprise sequences from the capital city (Recife) and other country-side cities, corroborating the community spread between different municipalities of the state. These findings demonstrate that different from Southeastern Brazilian states where the epidemics were majorly driven by one dominant lineage (B.1.1.28 or B.1.1.33), the early epidemic phase at the Pernambuco state was driven by multiple B.1.1 lineages seeded through both national and international traveling.

The emergence of SARS-CoV-2 in the human population has caused a huge pandemic that is still unfolding in many countries around the world. Multiple epicenters of the pandemic have emerged since the first pneumonia cases in Wuhan, first in Italy followed by the USA and Brazil. Up to now, Brazil is the second most affected country, however, genomic sequences of SARS-CoV-2 strains circulating in the country are restricted to some highly impacted states. Although the Pernambuco state, located in the Northeast Region, is the sixth most affected brazilian state and the second considering lethality rate, there is a lack of high quality genomic sequences from the strains circulating in this region. Here, we sequenced 38 strains of SARS-CoV-2 from patients presenting Covid-19 symptoms. Phylogenetic reconstructions revealed that three lineages were circulating in the state and 36 samples belong to B1.1 lineage. We detected two introductions from European countries and five clades, corroborating the community spread of the virus between different municipalities of the state. Finally, we detected that all except one strain showed the D614G spike protein amino acid change that may impact virus infectivity in human cells. Our study brought new light to the spread of SARS-CoV-2 strains in one of the most heavily impacted states of Brazil.