Brief dispersion of a putative B.1.1.28-derived SARS-CoV-2 lineage harboring additional N234P and E471Q spike protein mutations in individuals crossing the Argentina-Brazil border

Silva, Mariana Soares da; Gularte, Juliana Schons; Demoliner, Meriane; Hansen, Alana Witt; Heldt, Fágner Henrique; Filippi, Micheli; Luckmann, Cristiane Borba; Pereira, Vyctoria Malayhka de Abreu Góes; Vaucher, Rodrigo de Almeida; Barboza, Victor dos Santos; Giongo, Janice Luehring; Rosa, Renato; Rocha, Evelise Tarouco da; Goulart, Bruno Kilpp; Fernandes, Fernanda Dos Santos; Pinto, Juliana Maciel; Bolzan, Leandro Pergher; Weber, Matheus Nunes; Almeida, Paula Rodrigues de; Fleck, Juliane Deise; Spilki, Fernando Rosado

doi:10.1016/j.tmaid.2022.102390

Cited by 3 publications

(3 citation statements)

References 10 publications

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“…Studies conducted throughout the COVID-19 pandemic have reported high sensibility and specificity values of RT-qPCR in COVID-19 diagnosis [ 31 , 46 ]. Hence, it is a highly useful tool that provides a solid basis for developing novel diagnostic and surveillance methods in clinical and environmental samples [ 6 , 23 , 47 ]. The ability of carrageenan-mediated viral RNA extraction, as illustrated in Figure 9 , further emphasizes the biotechnological potential of this widely available subantarctic macroalgae.…”

Section: Resultsmentioning

confidence: 99%

Carrageenan from Gigartina skottsbergii: A Novel Molecular Probe to Detect SARS-CoV-2

et al. 2023

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The COVID-19 pandemic has caused an unprecedented health and economic crisis, highlighting the importance of developing new molecular tools to monitor and detect SARS-CoV-2. Hence, this study proposed to employ the carrageenan extracted from Gigartina skottsbergii algae as a probe for SARS-CoV-2 virus binding capacity and potential use in molecular methods. G. skottsbergii specimens were collected in the Chilean subantarctic ecoregion, and the carrageenan was extracted —using a modified version of Webber’s method—, characterized, and quantified. After 24 h of incubation with an inactivated viral suspension, the carrageenan’s capacity to bind SARS-CoV-2 was tested. The probe-bound viral RNA was quantified using the reverse transcription and reverse transcription loop-mediated isothermal amplification (RT-LAMP) methods. Our findings showed that carrageenan extraction from seaweed has a similar spectrum to commercial carrageenan, achieving an excellent proportion of binding to SARS-CoV-2, with a yield of 8.3%. Viral RNA was also detected in the RT-LAMP assay. This study shows, for the first time, the binding capacity of carrageenan extracted from G. skottsbergii, which proved to be a low-cost and highly efficient method of binding to SARS-CoV-2 viral particles.

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Section: Resultsmentioning

confidence: 99%

Carrageenan from Gigartina skottsbergii: A Novel Molecular Probe to Detect SARS-CoV-2

et al. 2023

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“…Whole‐genome sequencing (WGS) is paramount for understanding the evolution and genetic diversity of these circulating strains and detecting emerging variants like Omicron 8 . Rapid sequencing and analysis of SARS‐CoV‐2 genomes have supported our ability to monitor the emergence and spread of SARS‐CoV‐2 variants 9 . Methods for sequencing SARS‐CoV‐2 predominantly utilized imbricate amplicon approaches on the Illumina and Nanopore platforms.…”

Section: Introductionmentioning

confidence: 99%

“…8 Rapid sequencing and analysis of SARS-CoV-2 genomes have supported our ability to monitor the emergence and spread of SARS-CoV-2 variants. 9 Methods for sequencing SARS-CoV-2 predominantly utilized imbricate amplicon approaches on the Illumina and Nanopore platforms. Current methods for SARS-CoV-2 WGS, including the well-established Artic network protocol, primarily rely on short-read amplification and sequencing.…”

mentioning

confidence: 99%

Application of whole‐genome tiling array at Shanghai port, China: An alternative method for SARS‐CoV‐2 surveillance

Liu,

Wang,

Mao

et al. 2023

Journal of Medical Virology

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The ongoing coronavirus disease 2019 (COVID‐19) pandemic, driven by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), highlights the critical role of genomic surveillance in tracking rapidly spreading viruses and their evolving lineages. The emergence of the SARS‐CoV‐2 tiling array, a comprehensive tool capable of capturing the entire viral genome, has presented a promising avenue for variants. This study introduces the SARS‐CoV‐2 tiling array as a novel method for port inspection. Using next‐generation sequencing as a benchmark, 35 positive samples underwent sequencing through both methodologies, including the Alpha variant (B.1.1.7), Delta variants (AY.120, AY.122, AY.23.1), and Omicron variants (BA.1, BA.2, BA.2.75, BA.4, BA.5, BE.1, BF.7, BN.1, BQ.1, XBB.1) within the sample set. The whole‐genome tiling array demonstrated successful identification of various sublineages of SARS‐CoV‐2. The average sequencing coverage rates were 99.22% (96.82%−99.92%) for the whole‐genome tiling array and 98.56% (92.81%−99.59%) for Illumina sequencing, respectively. The match rates of these two methods ranged from 92.81%−99.59%, with an average rate of 98.56%. Among the benefits of the whole‐genome tiling array are its cost‐effectiveness and equipment simplification, making it particularly suitable for identifying SARS‐CoV‐2 variants in the front‐line inspection department. The aforementioned findings provide valuable insights into the surveillance of COVID‐19 and present a pragmatic solution for improving quarantine measures at entry points.

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SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis

Menezes

Fonseca

Araújo

et al. 2022

Viruses

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Several studies have monitored the SARS-CoV-2 variants in Brazil throughout the pandemic. Here, we systematically reviewed and conducted a scientometric analysis of the SARS-CoV-2 genomic surveillance studies using Brazilian samples. A Pubmed database search on October 2022 returned 492 articles, of which 106 were included. Ninety-six different strains were reported, with variant of concern (VOC) gamma (n = 35,398), VOC delta (n = 15,780), and the variant of interest zeta (n = 1983) being the most common. The top three states with the most samples in the published articles were São Paulo, Rio de Janeiro, and Minas Gerais. Whereas the first year of the pandemic presented primary circulation of B.1.1.28 and B.1.1.33 variants, consecutive replacements were observed between them and VOI zeta, VOC gamma, VOC delta, and VOC omicron. VOI mu, VOI lambda, VOC alpha, and VOC beta were also detected but failed to reach significant circulation. Co-infection, re-infection, and vaccine breakthrough reports were found. Article co-citation differed from the co-authorship structure. Despite the limitations, we expect to give an overview of Brazil’s genomic surveillance studies and contribute to future research execution.

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Brief dispersion of a putative B.1.1.28-derived SARS-CoV-2 lineage harboring additional N234P and E471Q spike protein mutations in individuals crossing the Argentina-Brazil border

Cited by 3 publications

References 10 publications

Carrageenan from Gigartina skottsbergii: A Novel Molecular Probe to Detect SARS-CoV-2

Carrageenan from Gigartina skottsbergii: A Novel Molecular Probe to Detect SARS-CoV-2

Application of whole‐genome tiling array at Shanghai port, China: An alternative method for SARS‐CoV‐2 surveillance

SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis

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