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

July 4 2022

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 competitive fitness. 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. More broadly, we analyze 944 combinations of geographic regions and time windows to demonstrate that the average Distinctiveness of a lineage in a country/time window is predictive of a greater than 20 percentage point future increase in infection prevalence after 56 days with an ROC AUC of 0.89. Finally, we find that positions that constitute known SARS-CoV-2 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.


Michiel JM Niesen, Karthik Murugadoss, Patrick J Lenehan, Aron Marchler-Bauer, Jiyao Wang, Ryan Connor, James Brister, AJ Venkatakrishnan, Venky Soundararajan

nference, Cambridge, MA 02142, USA NCBI, U.S. National Library of Medicine, NIH, Bethesda, MD 20894, USA

The National Center for Biotechnology Information


Correspondence to:

Venky Soundararajan (venky@nference.net)