Timely Monitoring of SARS-CoV-2 RNA Fragments in Wastewater Shows the Emergence of JN.1 (BA.2.86.1.1, Clade 23I) in Berlin, Germany

Bartel, Alexander; Grau, José Horacio; Bitzegeio, Julia; Werber, Dirk; Linzner, Nico; Schumacher, Vera; Garske, Sonja; Liere, Karsten; Hackenbeck, Thomas; Rupp, Sofia Isabell; Sagebiel, Daniel; Böckelmann, Uta; Meixner, Martin

doi:10.3390/v16010102

Cited by 13 publications

(4 citation statements)

References 16 publications

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“…It rapidly spread in the following weeks to most regions (Espinosa-Gongora et al, 2023). Genomic monitoring of SARS-CoV-2 in Berlin's wastewater identified JN.1 as early as September 2023 using an Illumina COVIDSeq Test (Bartel et al, 2024). Results from wastewater surveillance sequencing in Denmark, indicated that the BA.2.86 variant was circulating in the country at a low level in mid-August (Rasmussen et al, 2023).…”

Section: Discussionmentioning

confidence: 99%

“…The use of wastewater monitoring can provide a comprehensive approach to tracking the circulation and spread of different SARS-CoV-2 variants within a community or population (Bartel et al, 2024;Combe et al, 2024;Cutrupi et al, 2022;Espinosa-Gongora et al, 2023;Lipponen et al, 2024). This method provides a broader perspective beyond individual testing, offering insights into the overall viral landscape and aiding in the early detection of emerging variants (Sapoval et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

“…Beginning in August 2023 and in the following months, BA.2.86* was detected in wastewater samples from several countries, including Sweden, France, Denmark, Germany and Thailand (Espinosa-Gongora et al, 2023;Wurtzer et al, 2024;Bartel et al, 2024;Rasmussen et al, 2023;Wannigama et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

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Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis

Veneri,

Brandtner,

Mancini

et al. 2024

Food Environ Virol

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The emergence of new SARS-CoV-2 variants poses challenges to global surveillance efforts, necessitating swift actions in their detection, evaluation, and management. Among the most recent variants, Omicron BA.2.86 and its sub-lineages have gained attention due to their potential immune evasion properties. This study describes the development of a digital PCR assay for the rapid detection of BA.2.86 and its descendant lineages, in wastewater samples. By using this assay, we analyzed wastewater samples collected in Italy from September 2023 to January 2024. Our analysis revealed the presence of BA.2.86 lineages already in October 2023 with a minimal detection rate of 2% which then rapidly increased, becoming dominant by January 2024, accounting for a prevalence of 62%. The findings emphasize the significance of wastewater-based surveillance in tracking emerging variants and underscore the efficacy of targeted digital PCR assays for environmental monitoring.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis

Veneri,

Brandtner,

Mancini

et al. 2024

Food Environ Virol

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“…Sotrovimab serum half-life was improved by inserting the Met428Leu/Asn434Ser (LS) mutation (Xtend TM ) in the Fc region. Unlike with other half-life extended anti-Spike mAbs, this mutation does not impact the ADCC functions of sotrovimab, which are important for its activity against SARS-CoV-2 [ 7 , 8 , 9 ]. This mutation was previously used in the mAb ravulizumab (approved for paroxysmal nocturnal hemoglobinuria).…”

Section: Introductionmentioning

confidence: 99%

Sotrovimab: A Review of Its Efficacy against SARS-CoV-2 Variants

Focosi,

Casadevall,

Franchini

et al. 2024

Viruses

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Among the anti-Spike monoclonal antibodies (mAbs), the S-309 derivative sotrovimab was the most successful in having the longest temporal window of clinical use, showing a high degree of resiliency to SARS-CoV-2 evolution interrupted only by the appearance of the BA.2.86* variant of interest (VOI). This success undoubtedly reflects rational selection to target a highly conserved epitope in coronavirus Spike proteins. We review here the efficacy of sotrovimab against different SARS-CoV-2 variants in outpatients and inpatients, discussing both randomized controlled trials and real-world evidence. Although it could not be anticipated at the time of its development and introduction, sotrovimab’s use in immunocompromised individuals who harbor large populations of variant viruses created the conditions for its eventual demise, as antibody selection and viral evolution led to its eventual withdrawal due to inefficacy against later variant lineages. Despite this, based on observational and real-world data, some authorities have continued to promote the use of sotrovimab, but the lack of binding to newer variants strongly argues for the futility of continued use. The story of sotrovimab highlights the power of modern biomedical science to generate novel therapeutics while also providing a cautionary tale for the need to devise strategies to minimize the emergence of resistance to antibody-based therapeutics.

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Computational Assessment of Clinical Drugs against SARS‐CoV‐2: Foreseeing Molecular Mechanisms and Potent Mpro Inhibitors

Panda,

Pani,

Sen Gupta

et al. 2024

ChemPhysChem

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The emergence of new SARS‐CoV‐2 variants of concern (VOC) is a propulsion for accelerated potential therapeutic discovery. SARS‐CoV‐2’s main protease (Mpro), essential for host cell viral replication, is a pre‐eminent druggable protein target. Here, we perform extensive drug re‐profiling of the comprehensive Excelra database, which compiles various under‐trial drug candidates for COVID‐19 treatment. For mechanistic understanding, the most promising screened‐out molecules with targets are subjected to molecular dynamics (MD) simulations. Post‐MD analyses demonstrate Darunavir, Ponatinib, and Tomivosertib forming a stable complex with Mpro, characterized by less fluctuation of Cα atoms, smooth and stable root‐mean‐square deviation (RMSD), and robust contact with the active site residues. Likewise, they all have lower binding free energy with Mpro, demonstrating strong affinity. In free energy landscape profiles, the distances from His41 and Cys145 exhibit a single energy minima basin, implying their preponderance in proximity to Mpro’s catalytic dyad. Overall, the computational assessment earmarks promising candidates from the Excelra database, emphasizing on carrying out exhaustive biochemical experiments along with clinical trials. The work lays the foundation for potential therapeutic interventions in treating COVID‐19.

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Timely Monitoring of SARS-CoV-2 RNA Fragments in Wastewater Shows the Emergence of JN.1 (BA.2.86.1.1, Clade 23I) in Berlin, Germany

Cited by 13 publications

References 16 publications

Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis

Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis

Sotrovimab: A Review of Its Efficacy against SARS-CoV-2 Variants

Computational Assessment of Clinical Drugs against SARS‐CoV‐2: Foreseeing Molecular Mechanisms and Potent Mpro Inhibitors

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