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Quantifying the immunological distinctiveness of emerging SARS-CoV-2 variants in the context of prior regional herd exposure.

ABSTRACT: The COVID-19 pandemic has seen the persistent emergence of immune-evasive SARS-CoV-2 variants under the selection pressure of natural and vaccination-acquired immunity. However, it is currently challenging to quantify how immunologically distinct a new variant is compared to all the prior variants to which a population has been exposed. Here, we define "Distinctiveness" of SARS-CoV-2 sequences based on a proteome-wide comparison with all prior sequences from the same geographical region. We observe a correlation between Distinctiveness relative to contemporary sequences and future change in prevalence of a newly circulating lineage (Pearson r = 0.75), suggesting that the Distinctiveness of emergent SARS-CoV-2 lineages is associated with their epidemiological fitness. We further show that the average Distinctiveness of sequences belonging to a lineage, relative to the Distinctiveness of other sequences that occur at the same place and time (n = 944 location/time data points), is predictive of future increases in prevalence (Area Under the Curve, AUC = 0.88 [95% confidence interval 0.86 to 0.90]). By assessing the Delta variant in India versus Brazil, we show that the same lineage can have different Distinctiveness-contributing positions in different geographical regions depending on the other variants that previously circulated in those regions. Finally, we find that positions that constitute epitopes contribute disproportionately (20-fold higher than the average position) to Distinctiveness. Overall, this study suggests that real-time assessment of new SARS-CoV-2 variants in the context of prior regional herd exposure via Distinctiveness can augment genomic surveillance efforts.

SUBMITTER: Niesen MJM

PROVIDER: S-EPMC9308564 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:Exposure to both occupational and nonoccupational noise is recognized as a risk factor for noise-induced hearing loss (NIHL). Although audiologists routinely inquire regarding history of noise exposure, there are limited tools available for quantifying this history or for identifying those individuals who are at highest risk for NIHL. Identifying those at highest risk would allow hearing conservation activities to be focused on those individuals. PURPOSE:To develop a detailed, task-based questionnaire for quantifying an individual's annual noise exposure (ANE) arising from both occupational and nonoccupational sources (aim 1) and to develop a short screening tool that could be used to identify individuals at high risk of NIHL (aim 2). RESEARCH DESIGN:Review of relevant literature for questionnaire development followed by a cross-sectional descriptive and correlational investigation of the newly developed questionnaire and screening tool. STUDY SAMPLE:One hundred fourteen college freshmen completed the detailed questionnaire for estimating ANE (aim 1) and answered the potential screening questions (aim 2). An additional 59 adults participated in data collection where the accuracy of the screening tool was evaluated (aim 2). DATA COLLECTION AND ANALYSIS:In study aim 1, all participants completed the detailed questionnaire and the potential screening questions. Descriptive statistics were used to quantify participant participation in various noisy activities and their associated ANE estimates. In study aim 2, linear regression techniques were used to identify screening questions that could be used to predict a participant's estimated ANE. Clinical decision theory was then used to assess the accuracy with which the screening tool predicted high and low risk of NIHL in a new group of participants. RESULTS:Responses on the detailed questionnaire indicated that our sample of college freshmen reported high rates of participation in a variety of occupational and nonoccupational activities associated with high sound levels. Although participation rates were high, ANE estimates were below highest-risk levels for many participants because the frequency of participation in these activities was low in many cases. These data illustrate how the Noise Exposure Questionnaire (NEQ) could be used to provide detailed and specific information regarding an individual's exposure to noise. The results of aim 2 suggest that the screening tool, the 1-Minute Noise Screen, can be used to identify those participants with high- and low-risk noise exposure, allowing more in-depth assessment of noise exposure history to be targeted at those most at risk. CONCLUSIONS:The NEQ can be used to estimate an individual's ANE and the 1-Minute Noise Screen can be used to identify those participants at highest risk of NIHL. These tools allow audiologists to focus hearing conservation efforts on those individuals who are most in need of those services.

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Quantifying the immunological distinctiveness of emerging SARS-CoV-2 variants in the context of prior regional herd exposure.

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