VOC-alarm: mutation-based prediction of SARS-CoV-2 variants of concern

• DOI: 10.1093/bioinformatics/btac370
• Publication Date: 2022-06-01T00:43:12Z
• Authors: Hongyu Zhao; Kun Han; Chao Gao; Vithal Madhira; Umit Topaloglu; Yong Lu; Guangxu Jin
• Keywords: 03 medical and health sciences; 0302 clinical medicine; SARS-CoV-2; Mutation; Humans; COVID-19; Software; 3. Good health

ABSTRACT Summary Mutation is the key for a variant of concern (VOC) to overcome selective pressures, but this process still unclear. Understanding association mutational with VOCs an unmet need. Motivation: Here, we developed VOC-alarm, method predict and their caused COVID surges, using mutations about 5.7 million SARS-CoV-2 complete sequences. We found that rely on lineage-level entropy value mutation numbers compete other variants, suggestive importance population-level in virus evolution. Thus, hypothesized are result across globe. Results: Analyzing from January 2020 December 2021, simulated by estimating pace evolution, thus divided time period, 2020—March 2022, into eight stages. predicted Alpha, Delta, Delta Plus (AY.4.2) Omicron (B.1.1.529) values Stages I, III, V VII accelerated paces, respectively. In late November VOC-alarm alerted strongly competed plus become highly transmissible variant. Using data, also could lead another surge 2022 March 2022. Availability implementation Our software available at https://github.com/guangxujin/VOC-alarm. Supplementary information data Bioinformatics online.