Epidemiological investigation reveals local transmission of SARS-CoV-2 lineage P.1 in Southern Brazil

Salvato, Richard Steiner; Gregianini, Tatiana Schäffer; Campos, Aline Alves Scarpellini; Crescente, Lara Villanova; Vallandro, Marcelo Jostmeier; Ranieri, Tani Schilling; Vizeu, S.; Martins, Letícia Garay; Silva, Eduardo Viegas da; Pedroso, Ellen Regina; Burille, Andréia; Baethgen, Ludmila Fiorenzano; Schiefelbein, Sun Hee; Machado, Tiago; Becker, Irina Marieta; Ramos, Raquel Rocha; Piazza, Cláudia Fasolo; Nunes, Zenaida Marion Alves; Bastos, Cynthia Goulart Molina Bastos

doi:10.17058/reci.v1i1.16335

Cited by 9 publications

(5 citation statements)

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“…In the context of SARS-CoV-2 variants, the B.1.1.28 and P.1 lineages are highly found in Southern Brazil 17,18 and harbor important mutations in the virus spike protein. The emergence of B.1.1.28 lineage was described in November 2020 18 , while the P.1 (which derives from B.1.1.28) was first described in late January 2021 19 . Although our enrollment was completed in early November, it is unknown if these variants were present in our samples.…”

Section: Discussionmentioning

confidence: 99%

Children Have Similar Reverse Transcription Polymerase Chain Reaction Cycle Threshold for Severe Acute Respiratory Syndrome Coronavirus 2 in Comparison With Adults

Polese-Bonatto

Sartor

Varela

et al. 2021

Pediatric Infectious Disease Journal

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Section: Discussionmentioning

confidence: 99%

Children Have Similar Reverse Transcription Polymerase Chain Reaction Cycle Threshold for Severe Acute Respiratory Syndrome Coronavirus 2 in Comparison With Adults

Polese-Bonatto

Sartor

Varela

et al. 2021

Pediatric Infectious Disease Journal

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“…The P.1 lineage initiated a new wave of infections in Brazil around November 2020, starting in Manaus (northern Brazil) and spreading across the country (Faria et al, 2021). In RS, P.1 arrived in mid of January 2021, with a high transmission rate until April 2021, characterizing the second COVID-19 wave in the state (Varela et al, 2021; Salvato et al, 2021).…”

Section: Discussionmentioning

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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“…7,18,20,24,[39][40][41] In addition, both VOIs rapidly spread in the last 6 months. 7,8,19,20,24,[41][42][43] P.2 was first detected in July 2020 and represented 20% of all sequenced SARS-CoV-2 from this month until February 2021. Importantly, it increased from less than 10% in September 2020 to more than 30% of all lineages from October 2020 to February 2021.…”

Section: Discussionmentioning

confidence: 99%

“…P. This is further evidenced in some recent reports in different Brazilian regions. 5,7,8,19,20,22,24,41,43 Additionally, a recent epidemiological report from the São Paulo state demonstrated that more than 90% of the SARS-CoV-2 genomes sequenced in this state were P.1. 47 All these findings indicate that these lineages have been extremely important in the establishment of the second wave of the SARS-CoV-2 pandemic in Brazil.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, North and Southeast regions were fundamental for the emergence and fast spreading of these both SARS-CoV-2 VOIs. 5,7,8,[18][19][20]22,24,41,43 F I G U R E 4 (A) Time-scaled maximum clade credibility tree from the evolutionary reconstruction by Bayesian analysis of SARS-CoV-2 P.1 (Gamma) lineage whole-genome sequences from Brazil available in GISAID (from December 2020 to February 2021). The time of the most recent common ancestor (tMRCA) is demonstrated in the nodes with significant posterior probabilities (≥0.95).…”

Section: Discussionmentioning

confidence: 99%

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Temporal spread and evolution of SARS‐CoV‐2 in the second pandemic wave in Brazil

Wolf

Kipper

Borges

et al. 2021

Journal of Medical Virology

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Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil that presented more than 21 million coronavirus disease 2019 cases and 590 000 deaths.The recent emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide. The present study describes the temporal spreading and evolution of SARS-CoV2 in the beginning of the second pandemic wave in Brazil, highlighting the fast dissemination of the two major concerning variants (P.1 and P.2). A total of 2507 SARS-CoV-2 whole-genome sequences (WGSs) with available information from the country (Brazil) and sampling date (July 2020-February 2021), were obtained and the frequencies of the lineages were evaluated in the period of the growing second pandemic wave. The results demonstrated the increasing prevalence of P.1 and P.2 lineages in the period evaluated. P.2 lineage was first detected in the middle of 2020, but a high increase occurred only in the last trimester of this same year and the spreading to all Brazilian regions. P.1 lineage emerged even later, first in the North region in December 2020 and really fast dissemination to all other Brazilian regions in January and February 2021. All SARS-CoV-2 WGSs of P.1 and P.2 were further separately evaluated with a Bayesian approach. The rates of nucleotide and amino acid substitutions were statistically higher in P.1 than P.2 (p < 0.01). The phylodynamic analysis demon-

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Epidemiological investigation reveals local transmission of SARS-CoV-2 lineage P.1 in Southern Brazil

Cited by 9 publications

References 3 publications

Children Have Similar Reverse Transcription Polymerase Chain Reaction Cycle Threshold for Severe Acute Respiratory Syndrome Coronavirus 2 in Comparison With Adults

Children Have Similar Reverse Transcription Polymerase Chain Reaction Cycle Threshold for Severe Acute Respiratory Syndrome Coronavirus 2 in Comparison With Adults

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

Temporal spread and evolution of SARS‐CoV‐2 in the second pandemic wave in Brazil

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