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

Paiva, Marcelo Henrique Santos; Guedes, Duschinka Ribeiro Duarte; Docena, Cássia; Bezerra, Matheus Filgueira; Dezordi, Filipe Zimmer; Machado, Laís Ceschini; Krokovsky, Larissa; Helvécio, Elisama; Silva, Alexandre Freitas da; Vasconcelos, Luydson Richardson Silva; Rezende, Antônio Mauro; Silva, Severino Jefferson Ribeiro da; Sales, Kamila Gaudêncio da Silva; Sá, Bruna Santos Lima Figueiredo de; Cruz, Derciliano Lopes da; Cavalcanti, Claudio Eduardo; Menezes-Neto, Armando de; Silva, Caroline Targino Alves da; Mendes, Renata Pessôa Germano; Silva, Maria Almerice Lopes da; Barros, Michelle da Silva; Nascimento, Wheverton Ricardo Correia do; Loyo, Rodrigo Moraes; Bezerra, Luciane Caroline Albuquerque; Filho, Sinval Pinto Brandão; Ayres, Constância Flávia Junqueira; Wallau, Gabriel Luz

doi:10.1101/2020.08.25.20171595

Cited by 11 publications

(18 citation statements)

References 57 publications

(67 reference statements)

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“…Compared to three other studies conducted in Brazil (Candido et al 2020b), in the states of Minas Gerais (Xavier et al 2020) and Pernambuco (Paiva et al 2020) in the early phase of pandemic — which showed the introduction of viral lineages from other continents (mainly Europe) by international returning travelers —, this study suggests a minor role of international lineages in the ongoing viral transmission in Esteio. We speculate a trend towards the perpetuation and diversification of the lineages found in this study (B.1.1.248 and B.1.1.33) inside Brazil, unless new importations massively occur and these new imported lineages begin to circulate.…”

Section: Discussioncontrasting

confidence: 74%

“…Unprecedented international efforts of viral sequencing have allowed the submission of ∼375,000 genomes in the Global Initiative on Sharing All Influenza Data (GISAID) up to date (Shu and McCauley 2017), which are now available for studies of genomic epidemiology to follow the evolutionary history and dynamics of SARS-CoV-2 through space and time. In this sense, some important studies were already conducted in highly-affected countries, including China (Lu et al 2020), USA (Deng et al 2020; Fauver et al 2020; Ladner et al 2020; Maurano et al 2020), Italy (Bartolini et al 2020), Netherlands (Oude Munnink et al 2020), Australia (Rockett et al 2020; Seemann et al 2020), and Brazil (Candido et al 2020b; Paiva et al 2020; Xavier et al 2020).…”

Section: Introductionmentioning

confidence: 99%

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Genomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil

Franceschi

Caldana

Mayer

et al. 2021

Preprint

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Brazil is the third country most affected by Covid-19 pandemic. In spite of this, viral evolution in municipality resolution is poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. We identified four main circulating lineages in Esteio (Southern Brazil) and their relationship with global, national and regional lineages using phylogenetics and phylodynamics inferences from 21 SARS-CoV-2 genome sequences. We provided a comprehensive view of viral mutations from a time- and age-representative sampling from May to October 2020, in Esteio (RS, Brazil), highlighting two frequent mutations in Spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in Spike Receptor Binding Domain (RBD) characteristic of the South African lineage B.1.351, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). A significant viral diversity was evidenced with the identification of 80 different SNPs. The E484K replacement was found in two genomes (9.5%) from samples obtained in mid-October, which is to our best knowledge the earliest description of E484K harboring SARS-CoV-2 in South Brazil. This mutation identified in a small municipality from the RS state demonstrates that it was probably widely distributed in the Brazilian territory, but went unnoticed so far by the lack of genomic surveillance in Brazil. The introduction of E484K mutants shows temporal correlation with later increases in new cases in our state. Importantly, since it has been associated with immune evasion and enhanced interaction with hACE-2, lineages containing this substitution must be the subject of intense surveillance. Our date demonstrates multiple introductions of the most prevalent lineages (B.1.1.33 and B.1.1.248) and the major role of community transmission in viral spreading and the establishment of Brazilian lineages. This represents an important contribution to the epidemiology of SARS-CoV-2.

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Section: Discussioncontrasting

confidence: 74%

Section: Introductionmentioning

confidence: 99%

Genomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil

Franceschi

Caldana

Mayer

et al. 2021

Preprint

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“…A dynamic nomenclature system for SARS-CoV-2 can be used to track the lineages as they emerge and move in local and global patterns [ 19 ]. Phylogenetic and phylogeographic methods were used to track the early emergence of the virus in Italy [ 29 , 30 ]; New York [ 31 ]; and Pernambuco, Brazil [ 32 ]. In addition to tree inference, epidemic and sequence simulation methods established the earliest sustained transmission networks in Europe and the USA [ 33 ].…”

Section: Discussionmentioning

confidence: 99%

Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa

Engelbrecht

Delaney

Kleinhans

et al. 2021

Viruses

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Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing generated SARS-CoV-2 whole genomes. Phylogenetic inference with maximum likelihood and Bayesian methods were used to determine lineages that seeded the local epidemic. Three patients were known to have travelled internationally and an outbreak was detected in a nearby supermarket. Sequencing of 50 samples produced 46 high-quality genomes. The sequences were classified as lineages: B, B.1, B.1.1.1, B.1.1.161, B.1.1.29, B.1.8, B.39, and B.40. All the sequences from persons under investigation (PUIs) in the supermarket outbreak (lineage B.1.8) fall within a clade from the Netherlands with good support (p > 0.9). In addition, a new mutation, 5209A>G, emerged within the Cape Town cluster. The molecular clock analysis suggests that this occurred around 13 March 2020 (95% confidence interval: 9–17 March). The phylogenetic reconstruction suggests at least nine early introductions of SARS-CoV-2 into Cape Town and an early localized transmission in a shopping environment. Genomic surveillance was successfully used to investigate and track the spread of early introductions of SARS-CoV-2 in Cape Town.

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“…Many new SARS-CoV-2 strains associated with Spike substitutions have recently emerged (e.g. as observed for variants from Brazil, United-Kingdom and South-Africa) with increased infectivity (28)(29)(30)(31). These new strains also display several mutations in other viral genes encoding for structural and accessory proteins.…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV2 envelop proteins reshape the serological responses of COVID-19 patients

Martin

Heslan²,

Jégou

et al. 2021

Preprint

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The SARS-CoV-2 pandemic has elicited a unique international mobilization of the scientific community to better understand this coronavirus and its associated disease and to develop efficient tools to combat infection. Similar to other coronavirae, SARS-CoV-2 hijacks the host cell complex secretory machinery to produce properly folded viral proteins that will compose the nascent virions; including Spike, Envelope and Membrane proteins, the most exposed membrane viral proteins to the host immune system. Antibody response is part of the anti-viral immune arsenal that infected patients develop to fight viral particles in the body. Herein, we investigate the immunogenic potential of Spike (S), Envelope (E) and Membrane (M) proteins using a human cell-based system to mimic membrane insertion and N-glycosylation. We show that both S and M proteins elicit the production of specific IgG, IgM and IgA in SARS-CoV-2 infected patients. Elevated Ig responses were observed in COVID+ patients with moderate and severe forms of the disease. Finally, when SARS-CoV-2 Spike D614 and G614 variants were compared, reduced Ig binding was observed with the Spike G614 variant. Altogether, this study underlines the needs for including topological features in envelop proteins to better characterize the serological status of COVID+ patients, points towards an unexpected immune response against the M protein and shows that our assay could represent a powerful tool to test humoral responses against actively evolving SARS-CoV-2 variants and vaccine effectiveness.

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

Cited by 11 publications

References 57 publications

Genomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil

Genomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil

Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa

SARS-CoV2 envelop proteins reshape the serological responses of COVID-19 patients

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