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

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.

Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity

“…However, neutralization of the Brazilian/Japanese P.2 variant, whose RBD contains an E484K mutation, was significantly decreased (5.8-fold for BNT162b2, p < 0.001; 2.9-fold for mRNA-1273, p < 0.01) (Figures 4C-4D and S4A). This is in line with previous studies suggesting that the E484K mutation can evade polyclonal antibody responses (Greaney et al, 2021a;Jangra et al, 2021) and has been found in cases of SARS-CoV-2 reinfection (Paiva et al, 2020;Faria et al, 2021;Resende et al, 2021;Naveca et al, 2021;Vasques Nonaka et al, 2021). Similarly, neutralizing antibody responses were also significantly decreased for the Brazilian/Japanese P.1 strain (6.7-fold for BNT162b2, p < 0.0001; 4.5-fold for mRNA-1273, p < 0.001), Cell 184, 2372-2383, April 29, 2021 2375 Article which harbors three mutations in RBD (K417T, E484K, and N501Y) and has also been found in cases of reinfection (Faria et al, 2021).…”

“…Novel variants arising from the B.1.1.28 lineage first described in Brazil and Japan, termed P.2 (with 3 spike missense mutations) and P.1 (with 12 spike missense mutations), contain this E484K mutation, and P.1 in particular also contains K417T and N501Y mutations in RBD. These strains have been spreading rapidly, and both P.2 and P.1 were recently found in documented cases of SARS-CoV-2 reinfection (Paiva et al, 2020;Faria et al, 2021;Resende et al, 2021;Naveca et al, 2021;Vasques Nonaka et al, 2021).…”

Mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021: insights and limitations from uneven sequencing efforts

“…The states of Pernambuco (Northeast) and Minas Gerais (Southeast) presented more restricted viral dynamics. In Pernambuco, 88% of 101 early sequences were classified as lineage B.1.1 and six local B.1.1 clades were identified seeded through both national and international traveling (Paiva et al 2020) . This finding is consistent with the prevalence of B.1.1.74 lineage found in the Northeast, especially in Pernambuco.…”

“…Many studies were performed to characterize early viral introductions and transmission dynamics in several countries ( e. g. China (Lu et al 2020) , USA (Deng et al 2020;Worobey et al 2020;Maurano et al 2020) , Australia (Seemann et al 2020) , Italy (Bartolini et al 2020) , United Kingdom (da Silva Filipe et al 2021;du Plessis et al 2021) . In Brazil, SARS-CoV-2 arrived officially on February 25, 2020, in a returning traveller from Italy, and early efforts were made both at the national (Candido et al 2020b) and regional levels (Xavier et al 2020;Paiva et al 2020) to further characterize viral introduction and spread. B.1 and derived lineages were prevalent in the country at the beginning of the pandemic and significant movements between state borders after international travel restrictions have been demonstrated (Candido et al 2020b) .…”

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

“…The evolutionary position of the newly sequenced genomes was inferred using 1441 sequences from Brazil and 70 from other countries obtained from the GISAID database on February 25th, 2021. The Brazilian background sequences were selected following previous published protocol [13]. Modifications were clustering aligned sequences by 0.99985 similarity with CD-hit [14], keeping only the oldest record of each cluster and removing restrictions by country.…”