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. 2024 Feb 22;16(3):337.
doi: 10.3390/v16030337.

Evolution of a Distinct SARS-CoV-2 Lineage Identified during an Investigation of a Hospital Outbreak

Hosoon Choi  1 , Munok Hwang  1 , Lisa Cornelius  2 , Dhammika H Navarathna  3 , Piyali Chatterjee  1 , Chetan Jinadatha  2   4
Affiliations

Evolution of a Distinct SARS-CoV-2 Lineage Identified during an Investigation of a Hospital Outbreak

Hosoon Choi et al. Viruses. .

Abstract

The SARS-CoV-2 virus steadily evolves, and numerous antigenically distinct variants have emerged over the past three years. Tracking the evolution of the virus would help us understand the process that generates the diverse variants and predict the future evolutionary trajectory of SARS-CoV-2. Here, we report the evolutionary trajectory of a unique Omicron lineage identified during an outbreak investigation that occurred in a residence unit in the healthcare system. The new lineage had four distinct non-synonymous and two distinct synonymous mutations apart from its parental lineage. Since this lineage of virus was exclusively found during the outbreak, we were able to track the detailed evolutionary history of the entire lineage along the transmission path. Furthermore, we estimated the evolutionary rate of the SARS-CoV-2 Omicron variant from the analysis of the evolution of the lineage. This new Omicron sub-lineage acquired 3 mutations in a 12-day period, and the evolutionary rate was estimated as 3.05 × 10-3 subs/site/year. This study provides more insight into an ever-evolving virus.

Keywords: SARS-CoV-2; evolution; outbreak.

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Conflict of interest statement

We declare no competing interests.

Figures

Figure 1
Figure 1
Phylogenetic tree of 13 potential new lineage samples. Relative position of potential new lineage amongst the global samples, obtained from Nextstrain (https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_392fc_7cfc90.json?f_userOrOld=uploaded%20sample; accessed on 2 January 2024).
Figure 2
Figure 2
Position of mutations on the outbreak lineage. Synonymous mutations are marked with light blue arrows. Non-synonymous mutations are marked with red arrows. The three mutations that occurred during the outbreak are highlighted.
Figure 3
Figure 3
Cryo-EM structure of SARS-CoV-2 spike protein indicating the locations of mutations on each protomer. (A) Prefusion state of spike protein. HR2 domain is not included in the picture. (Adapted from RCSB PDB protein data bank; https://doi.org/10.2210/pdb7FCD/pdb [14]) (B) The folding of HR1 and HR2 of the S2 subunit during membrane fusion. Hydrophobic side chain of L1166 interacting with HR1. (Adapted from RCSB PDB protein data bank; https://doi.org/10.2210/pdb8CZI/pdb [15]).
Figure 4
Figure 4
Mutations along the transmission path based on collection date and sequence changes. The sample IDs in Groups A–D are listed in Table 1.
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Supplementary concepts

Grants and funding

This work was supported by a grant from the Office of Research and Development, The United States Department of Veterans Affairs as part of funding for VASeqCURE which in turn received funding from the American Rescue Plan Act funds and with additional support from Central Texas Veterans Health Care System, Temple, TX, USA.