Emergence of Crucial Evidence Catalyzing the Origin Tracing of SARS-CoV-2
Shunmei Chen, Cihan Ruan, Yutong Guo, Jia Chang, Haohao Yan, Liang Chen, Yongzhong Duan, Guangyou Duan, Jinlong Bei, Xin Li, Shan Gao
Abstract
Since the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), its genetic and geographical origins remain unclear, resulting in suspicions about its natural origin. In one of our previous studies, we reported the presence of a furin cleavage site RRAR in the junction region between S1 and S2 subunits of the spike protein, which was discovered as the first crucial clue for the origin tracing of SARS-CoV-2.
Introduction
Since the emergence of SARS-CoV-2, its genetic and geographical origins remain unclear, despite extensive research efforts. Several genomes of Sarbecovirus (also referred to as coronaviruses of betacoronavirus subgroups B) have provided significant clues for tracing the geographical origin of SARS-CoV-2. Among them, the genome of a notable strain RaTG13, isolated from intermediate horseshoe bats (Rhinolophus affinis), gained prominence shortly after the COVID-19 outbreak.
Materials and Methods:
The genus Betacoronavirus consists of five main subgenera Embecovirus, Sarbecovirus, Merbecovirus, Nobecovirus, and Hibecovirus which were defined as subgroups A, B, C, D, and E, respectively. In the previous study, 1,265 genome sequences of Betacoronavirus that had been generated and submitted before the COVID-19 outbreak were downloaded from the NCBI Virus database (https://www.ncbi.nlm.nih.gov/labs/virus). Among these genomes, 292 belonging to Sarbecovirus, were used in the present study for analysis.
Discussion
In our previous study, key genomic features were identified through the analysis of mutation sites in Sarbecovirus. Firstly, mutations were identified in the Sarbecovirus genomes, and then classified into two categories: small- and large-scale mutations. Small-scale mutations included single nucleotide substitutions (SNSs) and small insertions or deletions (InDels), whereas large-scale mutations included segment substitutions and large InDels involving at least 10 nucleotides.
Acknowledgments
We are grateful for the help from the following faculty members of College of Life Sciences at Nankai University: Wenjun Bu, Tao Zhang, Dawei Huang, Huaijun Xue, Qiang Zhao, Yanqiang Liu, Bingjun He, Wei Liu, and Zhen Ye. Special thanks should be given to Jinsong Shi from and National Clinical Research Center of Kidney Disease, Jinling Hospital and Alexandre Hassanin from Sorbonne Université. This manuscript has been submitted as a preprint on March 31st, 2024 at https://www.researchgate.net/ with acquisition of DOI: 10.13140/RG.2.2.23325.12008.
Citation: Chen S, Ruan C, Guo Y, Chang J, Yan H, Chen L, et al. (2024) Emergence of crucial evidence catalyzing the origin tracing of SARS-CoV-2. PLoS ONE 19(8): e0309557. https://doi.org/10.1371/journal.pone.0309557
Editor: AbdulAzeez Adeyemi Anjorin, Lagos State University, NIGERIA
Received: May 21, 2024; Accepted: August 13, 2024; Published: August 30, 2024.
Copyright: © 2024 Chen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the paper and its Supporting Information files.
Funding: The author(s) received no specific funding for this work.
Competing interests: The authors have declared that no competing interests exist.
