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Microbes & Immunity

SHORT COMMUNICATION
Comprehensive genomic surveillance analysis

of SARS-CoV-2: Global epidemic dynamics and
geographic variability of variants

Xingguang Li *, Haizhou Liu , and Yigang Tong *
1,2
4
3
1 Department of Emerging Infectious Diseases, Ningbo No. 2 Hospital, Ningbo, China
2 Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo,
China
3 National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences,
Wuhan, China
4 Department bioscience, College of Life Science and Technology, Beijing University of Chemical
Technology, Beijing, China

Abstract
Almost 4 years into the COVID-19 pandemic, the world has shifted into a phase
characterized by the Omicron variant, which has maintained prevalence for over a
year, giving rise to more than 3690 subvariants globally. To investigate the worldwide
genomic surveillance of SARS-CoV-2, metadata from over 5.5 million high-quality
genomes were analyzed. The results revealed significant geographic heterogeneity in
*Corresponding authors: the distribution of variants of concern/interest (VOC/VOI) across different continents,
Xingguang Li
(xingguanglee@hotmail.com) especially noticeable for the Epsilon and Iota VOIs. Moreover, the sequencing
Yigang Tong turnaround times exhibited notable geographic heterogeneity. These disparities
(tongyigang@mail.buct.edu.cn) in turnaround time and geographic coverage are critical for refining policies,
Citation: Li X, Liu H, Tong Y. guidelines, and mitigation strategies to effectively address the COVID-19 pandemic.
Comprehensive genomic In the context of the persistent COVID-19 pandemic and the global spread of various
surveillance analysis of SARS-
CoV-2: Global epidemic dynamics variants, understanding the mortality and transmissibility rates of SARS-CoV-2 is
and geographic variability of crucial. The mean mortality rate of SARS-CoV-2 stands at 2.62% (median: 2.17%; 95%
variants. Microbes & Immunity. confidence interval [CI]: 1.06 – 6.81%). Notably, the Omicron variant exhibits distinct
2024;1(1):2294.
doi: 10.36922/mi.2294 transmissibility characteristics (mean: 13.22; median: 12.06; 95% CI: 6.02 – 20.59)
compared to other SARS-CoV-2 variants (mean: 1.40; median: 1.12; 95% CI: 0.97 –
Received: November 22, 2023 2.28). These data underscore the need for future genomic surveillance strategies,
Accepted: December 13, 2021 including strategic sampling, randomized baseline surveillance, and rapid reporting,
Published Online: January 12, 2024 to enhance global public health efforts. Such strategies are essential for monitoring
and responding to the evolving landscape of the pandemic, as evidenced by the
Copyright: © 2024 Author(s). variability in mortality and transmission rates among different variants.
This is an Open-Access article
distributed under the terms of the
Creative Commons Attribution
License, permitting distribution, Keywords: SARS-CoV-2; Variants of concern/interest; Mortality rate; Submission lag;
and reproduction in any medium, Geographic heterogeneity
provided the original work is
properly cited.
Publisher’s Note: AccScience
Publishing remains neutral with Coronavirus disease 2019 (COVID-19) was initially identified in December 2019 in
regard to jurisdictional claims in
published maps and institutional Wuhan, Hubei Province, China, and was caused by severe acute respiratory syndrome
affiliations. coronavirus 2 (SARS-CoV-2). The ensuing pandemic has significantly impacted global

Volume 1 Issue 1 (2024) 106 doi: 10.36922/mi.2294