The first SARS-CoV-2 genetic variants of concern (VOC) in Poland: The concept of a comprehensive approach to monitoring and surveillance of emerging variants

Charkiewicz, Radosław; Nikliński, Jacek; Biecek, Przemysław; Kiśluk, Joanna; Pancewicz, Sławomir; Moniuszko‐Malinowska, Anna; Flisiak, Robert; Krętowski, Adam; Dzięcioł, J; Moniuszko, Marcin; Gierczyński, Rafał; Juszczyk, Grzegorz; Reszeć, Joanna

doi:10.1016/j.advms.2021.03.005

Cited by 11 publications

(10 citation statements)

References 17 publications

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“…It should also be noted that most of the breakthrough infections that are reported in the present study cannot be explained by immunosuppression or vaccine failure. Whether this is due to the emergence and spread of selected SARS-CoV-2 variants of concern (VOC), requires further studies [ 28 , 29 ]. As shown using the neutralization assays employing the sera of vaccinated individuals and pseudotyped virus, some variants, e.g., those possessing the E484K mutation in the receptor-binding domain, can potentially evade, to some extent, the immunity provided by the vaccines [ 30 ].…”

Section: Discussionmentioning

confidence: 99%

Clinical Characteristics of Hospitalized COVID-19 Patients Who Received at Least One Dose of COVID-19 Vaccine

et al. 2021

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The clinical trials of the COVID-19 vaccines that are authorized in the European Union have revealed high efficacy in preventing symptomatic infections. However, during vaccination campaigns, some vaccine recipients, including those partially and fully vaccinated, will experience severe COVID-19, requiring hospitalization. This may particularly concern patients with a diminished immune response to the vaccine, as well as non-responders. This work has retrospectively analyzed the 92 cases of patients who were hospitalized between 27 December 2020 and 31 May 2021 in four Polish healthcare units due to COVID-19, and who have previously received the COVID-19 vaccine (54.3% ≤ 14 days after the first dose, 26.1% > 14 days after the first dose, 7.6% ≤ 14 days after the second dose, and 12% > 14 days after the second dose). These patients represented a minute fraction (1.2%) of all the COVID-19 patients who were hospitalized during the same period in the same healthcare institutions. No significant differences in white blood count, absolute lymphocyte count nadir, C-reactive protein, interleukin-6, procalcitonin, oxygen saturation, lung involvement, and fever frequency were found between the recipients of the first and second vaccine dose. A total of 15 deaths were noted (1.1% of all fatal COVID-19 cases in the considered period and healthcare units), including six in patients who received the second dose (five > 14 days after the second dose)—three of these subjects were using immunosuppressive medicines, and two were confirmed to be vaccine non-responders. The study reassures that severe COVID-19 and deaths are not common in vaccinated individuals, highlights that the clinical course in such patients may not reveal any distinctive features, and advocates for close monitoring of those at a higher risk of vaccine failure.

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Section: Discussionmentioning

confidence: 99%

Clinical Characteristics of Hospitalized COVID-19 Patients Who Received at Least One Dose of COVID-19 Vaccine

et al. 2021

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“…There is a robust and expanding set of data characterizing the features of amino acid mutations occurring in viral variants of SARS-CoV-2. Studies have identified the emergence of new variants with altered biological and/or antigenic properties [8][9][10] and characterized them using low throughput methods 11,12 . Deep mutational scanning elucidates the in vitro biological effects of all single site amino acid substitutions [13][14][15] .…”

Section: Introductionmentioning

confidence: 99%

Predicting the mutational drivers of future SARS-CoV-2 variants of concern

Maher

Bartha

Weaver

et al. 2021

Preprint

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SARS-CoV-2 evolution threatens vaccine- and natural infection-derived immunity, and the efficacy of therapeutic antibodies. Herein we sought to predict Spike amino acid changes that could contribute to future variants of concern. We tested the importance of features comprising epidemiology, evolution, immunology, and neural network-based protein sequence modeling. This resulted in identification of the primary biological drivers of SARS-CoV-2 intra-pandemic evolution. We found evidence that resistance to population-level host immunity has increasingly shaped SARS-CoV-2 evolution over time. We identified with high accuracy mutations that will spread, at up to four months in advance, across different phases of the pandemic. Behavior of the model was consistent with a plausible causal structure wherein epidemiological variables integrate the effects of diverse and shifting drivers of viral fitness. We applied our model to forecast mutations that will spread in the future, and characterize how these mutations affect the binding of therapeutic antibodies. These findings demonstrate that it is possible to forecast the driver mutations that could appear in emerging SARS-CoV-2 variants of concern. This modeling approach may be applied to any pathogen with genomic surveillance data, and so may address other rapidly evolving pathogens such as influenza, and unknown future pandemic viruses.

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“…There is a robust and expanding set of analyses characterizing the features of amino acid mutations of SARS-CoV-2. Studies have identified the emergence of new variants with altered biological or antigenic properties (7)(8)(9) and characterized them using low-throughput methods (10,11). Deep mutational scanning elucidates the in vitro biological effects of all single site amino acid substitutions in a fixed genomic backbone (12)(13)(14).…”

mentioning

confidence: 99%

Predicting the mutational drivers of future SARS-CoV-2 variants of concern

et al. 2022

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INTRODUCTIONSARS-CoV-2 evolution presents an ongoing challenge to public health. Tens of thousands of mutations have arisen in the SARS-CoV-2 genome as the pandemic has progressed. Understanding the relative importance of mutations in viral proteins, particularly those of relevance for antiviral immunity, is key to allocating preparedness efforts. Mutations in the viral Spike protein have received particular attention because Spike is the target of antibody-mediated immunity and is the primary antigen in current vaccines (1). As of December 1st, 2021, there are 10,381 distinct amino acid substitutions, insertions, or deletions in Spike sequences from the GISAID database (2). These mutations occur at all but one position in the protein, in different combinations, creating over 160,000 unique Spike protein sequences. A small subset of these mutations are components of "Variants Being Monitored" (VBMs), "Variants of Interest" (VOIs) or "Variants of Concern" (VOCs), as classified by the United States Centers for Disease Control (CDC) (3). The distinction between VOIs and the higher alert VOCs is whether a negative clinical impact is suspected or confirmed. VBMs are variants that would be classified as VOCs if not for low prevalence.Early statistical and algorithmic identification of the key Spike amino acid changes contributing to future putative VBM/VOI/VOCs are of clear benefit to public health strategy. Such predictions could enhance the identification of vulnerabilities for antibody-based therapeutics, vaccines, and diagnostics. Predicting future successful mutations would extend the time available to develop proactive responses at earlier stages of spread. It would also complement existing forecasting efforts which seek to predict overall SARS-CoV-2 incidence, hospitalizations, and death over time (4-6). Focus on the success of individual mutations rather than genomic variants also facilitates longer-term forecasting. The

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The first SARS-CoV-2 genetic variants of concern (VOC) in Poland: The concept of a comprehensive approach to monitoring and surveillance of emerging variants

Cited by 11 publications

References 17 publications

Clinical Characteristics of Hospitalized COVID-19 Patients Who Received at Least One Dose of COVID-19 Vaccine

Clinical Characteristics of Hospitalized COVID-19 Patients Who Received at Least One Dose of COVID-19 Vaccine

Predicting the mutational drivers of future SARS-CoV-2 variants of concern

Predicting the mutational drivers of future SARS-CoV-2 variants of concern

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