TY - JOUR
T1 - VOC-alarm
T2 - mutation-based prediction of SARS-CoV-2 variants of concern
AU - Zhao, Hongyu
AU - Han, Kun
AU - Gao, Chao
AU - Madhira, Vithal
AU - Topaloglu, Umit
AU - Lu, Yong
AU - Jin, Guangxu
N1 - Funding Information:
This work was supported by a start-up fund from Wake Forest University Health Sciences. We also acknowledge assistance of the Wake Forest Baptist Comprehensive Cancer Center Bioinformatics Shared Resource, supported by [P30CA012197]. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Cancer Institute.
Funding Information:
This work was supported by a start-up fund from Wake Forest University Health Sciences. We also acknowledge assistance of the Wake Forest Baptist Comprehensive Cancer Center Bioinformatics Shared Resource, supported by [P30CA012197]. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Cancer Institute.
Publisher Copyright:
© 2022 The Author(s).
© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
PY - 2022/7/11
Y1 - 2022/7/11
N2 - SUMMARY: Mutation is the key for a variant of concern (VOC) to overcome selective pressures, but this process is still unclear. Understanding the association of the mutational process with VOCs is an unmet need. Motivation: Here, we developed VOC-alarm, a method to predict VOCs and their caused COVID surges, using mutations of about 5.7 million SARS-CoV-2 complete sequences. We found that VOCs rely on lineage-level entropy value of mutation numbers to compete with other variants, suggestive of the importance of population-level mutations in the virus evolution. Thus, we hypothesized that VOCs are a result of a mutational process across the globe. Results: Analyzing the mutations from January 2020 to December 2021, we simulated the mutational process by estimating the pace of evolution, and thus divided the time period, January 2020-March 2022, into eight stages. We predicted Alpha, Delta, Delta Plus (AY.4.2) and Omicron (B.1.1.529) by their mutational entropy values in the Stages I, III, V and VII with accelerated paces, respectively. In late November 2021, VOC-alarm alerted that Omicron strongly competed with Delta and Delta plus to become a highly transmissible variant. Using simulated data, VOC-alarm also predicted that Omicron could lead to another COVID surge from January 2022 to March 2022.AVAILABILITY AND IMPLEMENTATION: Our software implementation is available at https://github.com/guangxujin/VOC-alarm.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
AB - SUMMARY: Mutation is the key for a variant of concern (VOC) to overcome selective pressures, but this process is still unclear. Understanding the association of the mutational process with VOCs is an unmet need. Motivation: Here, we developed VOC-alarm, a method to predict VOCs and their caused COVID surges, using mutations of about 5.7 million SARS-CoV-2 complete sequences. We found that VOCs rely on lineage-level entropy value of mutation numbers to compete with other variants, suggestive of the importance of population-level mutations in the virus evolution. Thus, we hypothesized that VOCs are a result of a mutational process across the globe. Results: Analyzing the mutations from January 2020 to December 2021, we simulated the mutational process by estimating the pace of evolution, and thus divided the time period, January 2020-March 2022, into eight stages. We predicted Alpha, Delta, Delta Plus (AY.4.2) and Omicron (B.1.1.529) by their mutational entropy values in the Stages I, III, V and VII with accelerated paces, respectively. In late November 2021, VOC-alarm alerted that Omicron strongly competed with Delta and Delta plus to become a highly transmissible variant. Using simulated data, VOC-alarm also predicted that Omicron could lead to another COVID surge from January 2022 to March 2022.AVAILABILITY AND IMPLEMENTATION: Our software implementation is available at https://github.com/guangxujin/VOC-alarm.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
KW - Humans
KW - SARS-CoV-2/genetics
KW - COVID-19
KW - Mutation
KW - Software
UR - http://www.scopus.com/inward/record.url?scp=85134960659&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85134960659&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btac370
DO - 10.1093/bioinformatics/btac370
M3 - Article
C2 - 35640977
AN - SCOPUS:85134960659
SN - 1367-4803
VL - 38
SP - 3549
EP - 3556
JO - Bioinformatics
JF - Bioinformatics
IS - 14
ER -