Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 lineage (20H/501Y.V2) in Brazil (original) (raw)
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Journal of Medical Virology, 2021
Sao Paulo State, currently experiences a second COVID-19 wave overwhelming the healthcare system. Due to the paucity of SARS-CoV-2 complete genome sequencing, we established a Network for Pandemic Alert of Emerging SARS-CoV-2 Variants to rapidly understand and monitor the spread of SARS-CoV-2 variants into the state. Through analysis of 210 SARS-CoV-2 complete genomes obtained from the largest regional health departments we identified cocirculation of multiple SARS-CoV-2 lineages such as B.
Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil
PLOS Neglected Tropical Diseases, 2021
Tracking the spread of SARS-CoV-2 variants of concern is crucial to inform public health efforts and control the ongoing pandemic. Here, we report genetic evidence for circulation of the P.1 variant in Northeast Brazil. We advocate for increased active surveillance to ensure adequate control of this variant throughout the country.
Journal of Medical Virology, 2021
The appearance of new variants of SARS-CoV-2 has recently challenged public health authorities with respect to tracking transmission and mitigating the impact in the evolving pandemic across countries. B.1.525 is considered a variant under investigation since it carries specific genetic signatures present in P.1, B.1.1.7, and B.1.351. Here we report genomic evidence of the first likely imported case of the SARS-CoV-2 B.1.525 variant, isolated in a traveler returning from Nigeria.
Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil
2020
In this study, we report the sequencing of 180 new viral genomes obtained from different municipalities of the state of Rio de Janeiro from April to December 2020. We identified a novel lineage of SARS-CoV-2, originated from B.1.1.28, distinguished by five single-nucleotide variants (SNVs): C100U, C28253U, G28628U, G28975U, and C29754U. The SNV G23012A (E484K), in the receptor-binding domain of Spike protein, was widely spread across the samples. This mutation was previously associated with escape from neutralizing antibodies against SARS-CoV-2. This novel lineage emerged in late July being first detected by us in late October and still mainly restricted to the capital of the state. However, as observed for other strains it can be rapidly spread in the state. The significant increase in the frequency of this lineage raises concerns about public health management and continuous need for genomic surveillance during the second wave of infections.Article Summary LineWe identified a nove...
Genomic evidence of SARS-CoV-2 reinfection case with the emerging B.1.2 variant in Brazil
Journal of Infection, 2021
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SARS-CoV-2 Lineage P.4 Detection in Southeast Brazil: A Retrospective Genomic and Clinical Overview
COVID
São Paulo state has been the epicenter of the Coronavirus Disease 2019 (COVID-19) in Brazil, ranking first by state with over six million reported cases. In February 2021, the P.4 lineage was reported in 21 cities across the state by public health authorities due to the L452R mutation. Here, by analyzing 17,304 genome sequences of SARS-CoV-2 sampled between February and August of 2021 in 476 distinct cities in São Paulo, we assess the transmission dynamics of the P.4 lineage and other SARS-CoV-2 variants that were, at the time of the study, co-circulating in the state. Additionally, clinical parameters from the city of Araras, São Paulo (N = 251) were considered to estimate the potential risk and mortality rate associated with the P.4 lineage since its higher prevalence was observed in that city. Our data suggest a low frequency (0.55%) of the P.4 lineage across the state, with the gamma variant being the dominant form in all regions (90%) at that time. Furthermore, no evidence of i...
medRxiv (Cold Spring Harbor Laboratory), 2021
To provide a safer environment for individuals working on-site at the Federal University of Paraná, Curitiba, Brazil, we performed a large-scale mass testing SARS-CoV-2 program coupled with variant genotyping using two PCR-based approaches. We observed a fast dominance of the Gamma variant, displacing other variants in less than three months.. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) Text-word count 1199 Continuous screening for SARS-CoV-2 active infections, coupled with contact tracing, could efficiently reduce the viral transmission among the community(1). However, as virus variants with increased transmission emerge, a rise of cases within affected regions is observed, demanding immediate actions for blocking virus spread and consistent and continuous genomic surveillance for continuously evaluating vaccination approches(2). Brazil also showed consequences of the absence of genomic surveillance in a high seroprevalence scenario. Gamma (B.1.1.28/P.1) variant of concern (VOC) emerged in Manaus, Brazil, within threequarters of the population positive for anti-N IgG, rapidly spreading over the city(3). This new variant was able to displace his predecessor, the B.1.1.28/P.2 variant of interest (VOI), previously the major lineage, among the wild one(4). Extensive programs of routine asymptomatic screening for SARS-CoV-2 and follow-up sample genotyping are mandatory to control the cases and prevent further infection surges(5,6). The use of simplified approaches as multiplex qPCR provides a feasible, cost-effective way to discriminate samples and prioritize whole-genome sequencing efforts(5,7). In order to achieve this goal, we performed largescale surveillance of infections and VOCs in the Federal University of Paraná community (students, technicians, professors, outsourced workers, cohabitants, and their relatives). The study was approved by the Research Ethics Committee (CAAE: 31687620.2.0000.0096).
Pathogens, 2021
Almost a year after the COVID-19 pandemic had begun, new lineages (B.1.1.7, B.1.351, P.1, and B.1.617.2) associated with enhanced transmissibility, immunity evasion, and mortality were identified in the United Kingdom, South Africa, and Brazil. The previous most prevalent lineages in the state of Rio Grande do Sul (RS, Southern Brazil), B.1.1.28 and B.1.1.33, were rapidly replaced by P.1 and P.2, two B.1.1.28-derived lineages harboring the E484K mutation. To perform a genomic characterization from the metropolitan region of Porto Alegre, we sequenced viral samples to: (i) identify the prevalence of SARS-CoV-2 lineages in the region, the state, and bordering countries/regions; (ii) characterize the mutation spectra; (iii) hypothesize viral dispersal routes by using phylogenetic and phylogeographic approaches. We found that 96.4% of the samples belonged to the P.1 lineage and approximately 20% of them were assigned as the novel P.1.2, a P.1-derived sublineage harboring signature subst...