Quantifying the immunological distinctiveness of emerging SARS-CoV-2 variants in the context of prior regional herd exposure
This article has been Reviewed by the following groups
Discuss this preprint
Start a discussion What are Sciety discussions?Listed in
- Evaluated articles (ScreenIT)
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.
Article activity feed
-
-
SciScore for 10.1101/2022.03.06.22271974: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This study has a few limitations. First, SARS-CoV-2 genomic epidemiology is unfortunately impacted by major geographic and temporal sequencing biases. Over 55% of SARS-CoV-2 genome sequences in GISAID were isolated from infected patients in the United States or the United Kingdom, and the number of cases subjected to whole genome …
SciScore for 10.1101/2022.03.06.22271974: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This study has a few limitations. First, SARS-CoV-2 genomic epidemiology is unfortunately impacted by major geographic and temporal sequencing biases. Over 55% of SARS-CoV-2 genome sequences in GISAID were isolated from infected patients in the United States or the United Kingdom, and the number of cases subjected to whole genome sequencing increased massively starting at the end of 2020. Undersampling of SARS-CoV-2 genomes in other regions and/or during earlier months of the pandemic could impact our estimations of lineage Distinctiveness. Future analysis will include SARS-CoV-2 genomes from complementary databases such as the National Center for Biotechnology Information41. Second, it is not yet clear whether there exists a specific threshold for Distinctiveness (or change in Distinctiveness) that should be considered in the monitoring of future emerging lineages. Our retrospective observations show that sequential VOCs harbor progressively more distinctive amino acid content and are more distinctive than other lineages that were in circulation around their time of emergence, but it is worthwhile to continue prospectively investigating whether a particular degree of increased Distinctiveness is necessary for a new lineage to effectively spread within a region or across the globe. Third, Distinctiveness can be sensitive to sequence alignment parameters. Complementary analyses that are independent of sequence alignments are warranted to overcome this shortcoming. Finally, Dis...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-
