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MDPI, Viruses, 12(12), p. 1414, 2020

DOI: 10.3390/v12121414

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Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil

Journal article published in 2020 by Marcelo Henrique Santos Paiva ORCID, Duschinka Ribeiro Duarte Guedes, Cássia Docena, Matheus Filgueira Bezerra, Filipe Zimmer Dezordi ORCID, Laís Ceschini Machado, Larissa Krokovsky, Elisama Helvecio ORCID, Alexandre Freitas da Silva, Luydson Richardson Silva Vasconcelos, Antonio Mauro Rezende ORCID, Severino Jefferson Ribeiro da Silva ORCID, Kamila Gaudêncio da Silva Sales, Kamila Gaudêncio da Silva Sales, Wheverton Ricardo Correia do Nascimento and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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.