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Cheng XW, Li J, Zhang L, Hu WJ, Zong L, Xu X, Qiao JP, Zheng MJ, Jiang XW, Liang ZK, Zhou YF, Zhang N, Zhu HQ, Xu YH. Identification of SARS-CoV-2 Variants and Their Clinical Significance in Hefei, China. Front Med (Lausanne) 2022; 8:784632. [PMID: 35083244 PMCID: PMC8784789 DOI: 10.3389/fmed.2021.784632] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic represents one of the most exigent threats of our lifetime to global public health and economy. As part of the pandemic, from January 10 to March 10, 2020, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) began to spread in Hefei (Anhui Province, China) with a total of 174 confirmed cases of COVID-19. During this period, we were able to gather critical information on the transmission and evolution of pathogens through genomic surveillance. Particularly, the objective of our study was to track putative variants of SARS-CoV-2 circulating in Hefei for the first time and contribute to the global effort toward elucidating the molecular epidemic profile of the virus. Patients who showed symptoms of COVID-19 were routinely tested for SARS-CoV-2 infections via RT-PCR at the First Affiliated Hospital of Anhui Medical University. Whole-genome sequencing was performed on 97 clinical samples collected from 29 confirmed COVID-19 patients. As a result, we identified a local novel single-nucleotide polymorphism site (10,380) harboring a G → T mutation (Gly → Val) in Hefei. Further phylogenetic network analysis with all the sequences of SARS-CoV-2 deposited in GenBank collected in East and Southeast Asia revealed a local subtype of S-type SARS-CoV-2 (a1) harboring a C → T synonymous mutation (Leu) at position 18,060 of ORF1b, likely representing a local SARS-CoV-2 mutation site that is obviously concentrated in Hefei and the Yangtze River Delta region. Moreover, clinical investigation on the inflammatory cytokine profile of the patients suggested that mutations at positions 18,060 (the shared variable site of subtype a1) and 28,253(harboring a C → T synonymous mutation, Phe) were associated with milder immune responses in the patients.
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Affiliation(s)
- Xiao-Wen Cheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Laboratory of Molecular Biology, Department of Biochemistry, Anhui Medical University, Hefei, China
| | - Jie Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lu Zhang
- College of Life Sciences, Anhui Medical University, Hefei, China
| | - Wen-Jun Hu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lu Zong
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiang Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jin-Ping Qiao
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Mei-Juan Zheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xi-Wen Jiang
- Da An Gene Co., Ltd., Sun Yat-sen University, Guangzhou, China.,The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
| | - Zhi-Kun Liang
- Clinical Laboratory Center, Guangzhou Darui Biotechnology, Co., Ltd., Guangzhou, China
| | - Yi-Fan Zhou
- Division of Life Sciences and Medicine, Department of Pathology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
| | - Ning Zhang
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Hua-Qing Zhu
- Laboratory of Molecular Biology, Department of Biochemistry, Anhui Medical University, Hefei, China
| | - Yuan-Hong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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