Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil

Gräf, Tiago; Bello, Gonzalo; Naveca, Felipe Gomes; Gomes, Marcelo Ferreira da Costa; Cardoso, Vanessa Leiko Oikawa; Silva, Alexandre Freitas da; Dezordi, Filipe Zimmer; Santos, Mirleide Cordeiro dos; Oliveira, Mona N.; Batista, Érika Lopes Rocha; Magalhães, Alessandro Leonardo Álvares; Vinhal, Fernando; Miyajima, Fábio; Faoro, Helisson; Khouri, Ricardo; Wallau, Gabriel Luz; Delatorre, Edson; Siqueira, Marilda Mendonça; Resende, Paola Cristina; Mattos, Tirza; Nascimento, Valdinete Alves do; Souza, Victor Costa de; Corado, André de Lima Guerra; Nascimento, Fernanda; Silva, George; Mejía, Matilde; Brandão, Maria Júlia; Costa, Ana Carolina Carioca da; Pessoa, Karina; Jesus, Michele Silva de; Gonçalves, Luciana; Fernandes, Cristiano; Andrade, Valnete; Barbagelata, Luana Soares; Cruz, Ana Cecília Ribeiro; Costa, Andrea; Silva, Lindomar dos Anjos; Galvão, Jucimária Dantas; Leite, Anderson Brandão; Pereira, Felicidade Mota; Costa, Thais Oliveira; Sousa, Joaquim Cesar; Neto, Lídio Gonçãlves Lima; Barroso, Haline; Teixeira, Dalane Loudal Florentino; Bezerra, João Felipe; Docena, Cássia; Lima, Raul Emídio de; Silva, Lílian Caroliny Amorim; Lima, Gustavo Barbosa de; Machado, Laís Ceschini; Bezerra, Matheus Filgueira; Paiva, Marcelo Henrique Santos; Dantas, Maria Eduarda Pessoa Lopes; Pereira, Raíssa Liane Do Nascimento; Araújo, Josélio Maria Galvão de; Santos, Cliomar Alves do; Ribeiro‐Rodrigues, Rodrigo; Bernardes, André Felipe Leal; Iani, Felipe Campos de Melo; Grinsztejn, Beatriz; Veloso, Valdiléa G.; Brasil, Patrícia; Paixão, Ariane Gomes; Appolinario, Luciana; Lopes, Renata Serrano; Motta, Fernando do Couto; Rocha, Alice Sampaio Barreto da; Venas, Tainá Moreira Martins; Pereira, Elisa Cavalcante; Cavalcanti, Andréa Cony; Bastos, Leonardo Soares; Brígido, Luis Fernando de Macedo; Oliveira, Mauro de; Schemberger, Michelle Orane; Suzukawa, Andréia Akemi; Riediger, Irina Nastassja; Debur, Maria do Carmo; Salvato, Richard Steiner; Gregianini, Tatiana Schäffer; Rovaris, Darcita Büerger; Fernandes, Sandra Bianchini

doi:10.1016/j.isci.2022.104156

Cited by 21 publications

(20 citation statements)

References 38 publications

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“…Likewise, the same was observed in other Brazilian states [50,51]. After the origin of Gamma lineage on Amazonas state in the late November of 2020 [27], the subsequent spreading to other Brazilian states occurred mainly between December of 2020 and March of 2021 [52]. Current studies estimate the entry of Gamma lineage in the Northeast region varies from the middle-late December of 2020 [52] to early January 2021 [21] which is consistent with the tMRCA of the Gamma lineage in the Pernambuco state (1st December 2020 [95% high posterior density (HPD): 7th November 2020 -6th January 2021 Figure 3A).…”

Section: Sars-cov-2 Clades Detected In Pernambuco Statesupporting

confidence: 73%

“…After the origin of Gamma lineage on Amazonas state in the late November of 2020 [27], the subsequent spreading to other Brazilian states occurred mainly between December of 2020 and March of 2021 [52]. Current studies estimate the entry of Gamma lineage in the Northeast region varies from the middle-late December of 2020 [52] to early January 2021 [21] which is consistent with the tMRCA of the Gamma lineage in the Pernambuco state (1st December 2020 [95% high posterior density (HPD): 7th November 2020 – 6th January 2021 Figure 3A ). Regarding the root ages of Gamma clades that seeded large transmission chains in the state, our analysis estimates that they date back between early February 2021 (clade 12, Table 1 ) and mid April 2021 ( Figure 3A, Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

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Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco - Brazil

Machado

Dezordi

Lima

et al. 2023

Preprint

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In recent years, the SARS-CoV-2 viruses emerged and spread around the world, leaving a large death toll and long-lasting impact on survivors. As of January 2023, Brazil is still among the countries with the highest number of registered deaths. This continental-size and pluralistic country experienced a heterogenous implementation of non-pharmacological and pharmacological interventions which, associated with large socioeconomic differences between the country regions, has led to distinct virus spread dynamics across the country. Here we investigate the spatiotemporal dispersion of emerging SARS-CoV-2 lineages and its dynamics in distinct epidemiological scenarios in the first two years of the pandemics in the Pernambuco state (Northeast Brazil). We generated a total of 1389 new SARS-CoV-2 genomes from June 2020 to August 2021 covering all major regions of the state. This sampling captured the arrival, communitary transmission and the circulation of the B1.1, B.1.1.28 and B.1.1.33 lineages in the first eight months of the pandemics, the emergence of the former variant of interest P.2 and the emergence and fast replacement of all previous variants by the more transmissible variant of concern P.1 (Gamma) lineage. Based on the incidence and lineage spread pattern we observed that there was an East-to-West to inner state pattern of transmission which is in agreement with the transmission of more populous metropolitan areas to medium and small size country-side cities in the state. Such transmission patterns may be partially explained by the main routes of traffic across municipalities in the state. Nevertheless, inter-state traffic was also another important source of lineage introduction and spread into the state. Our results highlight that the fine grained intrastate analysis of lineages and incidence spread can provide actionable insights for planning future non-pharmacological intervention for air-borne transmissible human pathogens.

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Section: Sars-cov-2 Clades Detected In Pernambuco Statesupporting

confidence: 73%

Section: Resultsmentioning

confidence: 99%

Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco - Brazil

Machado

Dezordi

Lima

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

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“…Among several lineages, along these two years of pandemic, various Variants of Concern (VOCs), such as Alpha, Beta, Gamma, Delta, and Omicron, carrying signature aminoacid substitutions (especially in the spike protein) circulated in RS state (Gularte et al, 2022; Wink et al, 2022; Gräf et al, 2022). The sublineage P.1.2, a Gamma-like variant also considered as a Variant of Interest, was initially identified in RS state (Franceschi et al, 2021), despite other studies estimating its divergence between late 2020 and early 2021 in São Paulo state (Junior et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Genomic characterization and molecular evolution of SARS-CoV-2 in Rio Grande do Sul State, Brazil

Mayer

Ferrareze²,

Oliveira³

et al. 2023

Preprint

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The SARS-CoV-2 is the virus responsible for the COVID-19 pandemic and is plaguing the world since the end of 2019. Different lineages have been discovered ever since and the Gamma lineage, which started the second wave of infections, was first described in Brazil, one of the most affected countries by pandemic. Describing the viral genome and how the virus behaves is essential to contain its propagation and to the development of medications and vaccines. Therefore, this study analyzed SARS-CoV-2 sequenced genomes from Esteio city in Rio Grande do Sul, Southern Brazil. We also comparatively analyzed genomes of the two first years of the pandemic from Rio Grande do Sul state for understanding their genomic and evolutionary patterns. The phylogenomic analysis showed monophyletic groups for Alpha, Gamma, Delta and Omicron, as well as for other circulating lineages in the state. Molecular evolutionary analysis identified several sites under adaptive selection in membrane and nucleocapsid proteins which could be related to a prevalent stabilizing effect on membrane protein structure, as well as majoritarily destabilizing effects on C-terminal nucleocapsid domain.

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“…Many studies have been conducted in genomic epidemiology to find the transmission dynamics of COVID-19 in different cities and lineages of the virus [ 74 , 75 , 76 , 77 ]. These studies can see how many different lineages are responsible for affecting each city or country and which lineages are more deadly, more transmissible, and faster.…”

Section: Results and Interpretationmentioning

confidence: 99%

“…These studies can see how many different lineages are responsible for affecting each city or country and which lineages are more deadly, more transmissible, and faster. For example, one study estimated that lineage Gamma is 1.56 to 3.06 times more contagious than P.2 in Rio de Janeiro [ 74 ]. Moreover, the effective reproduction number of Gamma varies with geographic context.…”

Section: Results and Interpretationmentioning

confidence: 99%

Modeling COVID-19 Transmission Dynamics: A Bibliometric Review

Goswami

Labib

2022

IJERPH

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A good amount of research has evolved just in three years in COVID-19 transmission, mortality, vaccination, and some socioeconomic studies. A few bibliometric reviews have already been performed in the literature, especially on the broad theme of COVID-19, without any particular area such as transmission, mortality, or vaccination. This paper fills this gap by conducting a bibliometric review on COVID-19 transmission as the first of its kind. The main aim of this study is to conduct a bibliometric review of the literature in the area of COVID-19 transmission dynamics. We have conducted bibliometric analysis using descriptive and network analysis methods to review the literature in this area using RStudio, Openrefine, VOSviewer, and Tableau. We reviewed 1103 articles published in 2020–2022. The result identified the top authors, top disciplines, research patterns, and hotspots and gave us clear directions for classifying research topics in this area. New research areas are rapidly emerging in this area, which needs constant observation by researchers to combat this global epidemic.

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Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil

Cited by 21 publications

References 38 publications

Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco - Brazil

Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco - Brazil

Genomic characterization and molecular evolution of SARS-CoV-2 in Rio Grande do Sul State, Brazil

Modeling COVID-19 Transmission Dynamics: A Bibliometric Review

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