Multiple introductions followed by ongoing community spread of SARS-CoV-2 at one of the largest metropolitan areas in the Northeast of Brazil

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 Sa, 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.; Barros, M. d. S.; do Nascimento, W. R. C.; Arcoverde, R. M. L.; Bezerra, L. C. A.; Filho, S. P. B.; Ayres, C. F. J.; Wallau, G. L.

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.