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Article

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

1
Núcleo de Ciências da Vida, Universidade Federal de Pernambuco (UFPE), Centro Acadêmico do Agreste-Rodovia BR-104, km 59-Nova Caruaru, Caruaru 55002-970, Brazil
2
Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
3
Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
4
Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
5
Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
6
Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
7
Laboratório de Virologia e Terapia Experimental (LAVITE), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
8
Departamento de Imunologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
9
Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
10
Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
11
Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
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Departamento de Medicina Tropical, Centro de Ciências Médicas, Universidade Federal de Pernambuco (UFPE), Recife 50670-901, Brazil
13
Secretaria de Saúde de Pernambuco (SES-PE), Secretaria Executiva de Vigilância em Saúde (SEVS-PE), Recife 50751-530, Brazil
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editors: Luciana Barros de Arruda, Fabrício S. Campos and Flavio Guimaraes da Fonseca
Viruses 2020, 12(12), 1414; https://doi.org/10.3390/v12121414
Received: 17 October 2020 / Revised: 16 November 2020 / Accepted: 22 November 2020 / Published: 9 December 2020
(This article belongs to the Special Issue Viral Infections in Developing Countries)
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. View Full-Text
Keywords: SARS-CoV2; coronavirus; outbreak; Brazil; phylogenetics SARS-CoV2; coronavirus; outbreak; Brazil; phylogenetics
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Figure 1

MDPI and ACS Style

Paiva, M.H.S.; Guedes, D.R.D.; Docena, C.; Bezerra, M.F.; Dezordi, F.Z.; Machado, L.C.; Krokovsky, L.; Helvecio, E.; da Silva, A.F.; Vasconcelos, L.R.S.; Rezende, A.M.; da Silva, S.J.R.; Sales, K.G.d.S.; de Sá, B.S.L.F.; da Cruz, D.L.; Cavalcanti, C.E.; Neto, A.d.M.; da Silva, C.T.A.; Mendes, R.P.G.; da Silva, M.A.L.; Gräf, T.; Resende, P.C.; Bello, G.; Barros, M.d.S.; do Nascimento, W.R.C.; Arcoverde, R.M.L.; Bezerra, L.C.A.; Brandão-Filho, S.P.; Ayres, C.F.J.; Wallau, G.L. Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil. Viruses 2020, 12, 1414. https://doi.org/10.3390/v12121414

AMA Style

Paiva MHS, Guedes DRD, Docena C, Bezerra MF, Dezordi FZ, Machado LC, Krokovsky L, Helvecio E, da Silva AF, Vasconcelos LRS, Rezende AM, da Silva SJR, Sales KGdS, de Sá BSLF, da Cruz DL, Cavalcanti CE, Neto AdM, da Silva CTA, Mendes RPG, da Silva MAL, Gräf T, Resende PC, Bello G, Barros MdS, do Nascimento WRC, Arcoverde RML, Bezerra LCA, Brandão-Filho SP, Ayres CFJ, Wallau GL. Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil. Viruses. 2020; 12(12):1414. https://doi.org/10.3390/v12121414

Chicago/Turabian Style

Paiva, Marcelo H.S., Duschinka R.D. Guedes, Cássia Docena, Matheus F. Bezerra, Filipe Z. Dezordi, Laís C. Machado, Larissa Krokovsky, Elisama Helvecio, Alexandre F. da Silva, Luydson R.S. Vasconcelos, Antonio M. Rezende, Severino J.R. da Silva, Kamila G.d.S. Sales, Bruna S.L.F. de Sá, Derciliano L. da Cruz, Claudio E. Cavalcanti, Armando d.M. Neto, Caroline T.A. da Silva, Renata P.G. Mendes, Maria A.L. da Silva, Tiago Gräf, Paola C. Resende, Gonzalo Bello, Michelle d.S. Barros, Wheverton R.C. do Nascimento, Rodrigo M.L. Arcoverde, Luciane C.A. Bezerra, Sinval P. Brandão-Filho, Constância F.J. Ayres, and Gabriel L. Wallau 2020. "Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil" Viruses 12, no. 12: 1414. https://doi.org/10.3390/v12121414

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