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

Author:

Paiva Marcelo Henrique SantosORCID,Guedes Duschinka Ribeiro Duarte,Docena Cássia,Bezerra Matheus Filgueira,Dezordi Filipe ZimmerORCID,Machado Laís Ceschini,Krokovsky Larissa,Helvecio ElisamaORCID,da Silva Alexandre Freitas,Vasconcelos Luydson Richardson Silva,Rezende Antonio MauroORCID,da Silva Severino Jefferson RibeiroORCID,Sales Kamila Gaudêncio da Silva,de Sá Bruna Santos Lima Figueiredo,da Cruz Derciliano Lopes,Cavalcanti Claudio Eduardo,Neto Armando de MenezesORCID,da Silva Caroline Targino AlvesORCID,Mendes Renata Pessôa Germano,da Silva Maria Almerice Lopes,Gräf TiagoORCID,Resende Paola Cristina,Bello GonzaloORCID,Barros Michelle da Silva,do Nascimento Wheverton Ricardo Correia,Arcoverde Rodrigo Moraes Loyo,Bezerra Luciane Caroline Albuquerque,Brandão-Filho Sinval PintoORCID,Ayres Constância Flávia Junqueira,Wallau Gabriel LuzORCID

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.

Publisher

MDPI AG

Subject

Virology,Infectious Diseases

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