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Comment
. 2023 Jun;86(6):588-592.
doi: 10.1016/j.jinf.2023.03.003. Epub 2023 Mar 6.

Emergence of epidemic variants of SARS-CoV-2 by acquiring combinations of new highly mutable nucleotides in its genome

Hui Wang  1 , Yuqi Liu  2 , Peng Li  2 , Chaowu Liu  3 , Kuibiao Li  4 , Lan Cao  4 , Ying Zhang  4 , Zichun Cheng  1 , Kailing Huang  5 , Zhouxia Zheng  5 , Xiaoqian Xin  1 , Yifeng Liu  1 , Xiaofang Peng  6 , Dan Liang  6 , Bixia Ke  6 , Tao Wang  7 , Qingpei Chen  8 , Weihua Luo  9 , Chaolang Qin  9 , Lihong Sun  10 , Guobing Chen  11 , Oscar Junhong Luo  12 , Jixi Li  13 , Qiao Zhang  1 , Biao Di  4 , Zhoubin Zhang  14 , Changwen Ke  15 , Hongling Jia  16 , Feng Gao  17
Affiliations
Comment

Emergence of epidemic variants of SARS-CoV-2 by acquiring combinations of new highly mutable nucleotides in its genome

Hui Wang et al. J Infect. 2023 Jun.
No abstract available

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Conflict of interest statement

Declaration of Competing Interest The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Genetic and biological characterization of the new Delta-x variant. (A) Delta-x signature mutations (red) were the highest among all three possible mutations (black) at each position. (B) Frequencies of all mutations in the SARS-CoV-2 genomes. All mutations and Delta-x signature mutations are shown in blue squares and red dots, respectively, while all others are shown as gray open circles. (C) Percentage of the highly mutable Delta-x signature mutations is shown in red, while other two mutations are shown in blue and green, respectively. A total of 1,698,654 sequences (collected before May 21, 2021) were used for analysis. (D) Sequences with different numbers of the combined Delta-x signature mutations. (E) Analysis of the predominant haplotypes with different numbers of mutations among total sequences with the same number of mutations and total sequences with any mutations. (F) Viral replication kinetics was monitored by measuring viral RNA copy numbers in the cell culture supernatants using RT-qPCR. (G) Viral fitness was compared between the Delta-x and Delta viruses by determining the proportion of each virus in the same culture using NGS. (H) Neutralization of the Delta-x virus. The neutralization susceptibility of the Delta-x to convalescent sera from individuals infected with original viruses (n = 23) or Delta-x (n = 20) was compared to those of the Delta and Alpha viruses.
Fig. 2
Fig. 2
Number of all three possible mutations at each signature mutation site. The numbers of the highly mutable signature mutations in each VOC are shown in red, while other two mutations are shown in blue and green, respectively. The numbers of sequences used for Beta (A), Alpha (B), Delta (C), Gamma (D), and Omicron (E) are 1152, 6969, 6969, 73733, and 473719, respectively. An asterisk indicates one sequence at the position.
See this image and copyright information in PMC

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References

    1. Caillard S., Laugel E., Benotmane I., Kremer S.F. Molecular evolution of the SARS-CoV-2 omicron BA.2 variant in kidney transplant recipients with prolonged viral shedding. J Infect. 2023 doi: 10.1016/j.jinf.2023.02.001. - DOI - PMC - PubMed
    1. Domingo P., de Benito N. Alpha variant SARS-CoV-2 infection: how it all starts. EBioMedicine. 2021;74 doi: 10.1016/j.ebiom.2021.103703. - DOI - PMC - PubMed
    1. Callaway E. Delta coronavirus variant: scientists brace for impact. Nature. 2021;595(7865):17–18. doi: 10.1038/d41586-021-01696-3. - DOI - PubMed
    1. Karim S.S.A., Karim Q.A. Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic. Lancet. 2021;398(10317):2126–2128. doi: 10.1016/S0140-6736(21)02758-6. - DOI - PMC - PubMed
    1. Grifoni A., Sidney J., Vita R., Peters B., Crotty S., Weiskopf D., et al. SARS-CoV-2 human T cell epitopes: adaptive immune response against COVID-19. Cell Host Microbe. 2021;29(7):1076–1092. doi: 10.1016/j.chom.2021.05.010. - DOI - PMC - PubMed