Forensic Analysis of Novel SARS2r-CoV Identified in Game Animal Datasets in China Shows Evolutionary Relationship to Pangolin GX CoV Clade and Apparent Genetic Experimentation
Abstract
:1. Introduction
2. Methods
2.1. Consensus Genome
2.2. Viral Alignments
2.3. Phylogenetic Analyses
2.4. SimPlot Analyses
- SimPlot++ groups for GX_ZC45r query plot, genome as named except:
- ZXC21: bat-SL-CoVZXC21, ZC45: bat-SL-CoVZC45, PCoV_GX: PCoV_GX-P4L, PCoV_GD: PCoV_MP789, HKU3: HKU3-1, FJ2021: FJ2021D, AH2021: AH2021A.
- SimPlot++ groups for PCoV GX (PCoV_GX: GX_P2V, PCoV_GX-P1E, PCoV_GX-P4L, PCoV_GX-P5E, PCoV_GX-P5L) query plot, single genomes except for these groups: PCoV_GD: PCoV_A22-2, PCoV_MP789, PCoV_SM44-9, PCoV_SM79-9, BANAL: BANAL-20-103/Laos/2020, BANAL-20-116/Laos/2020, BANAL-20-236/Laos/2020, BANAL-20-236/Laos/2020, BANAL-20-247/Laos/2020, BANAL-20-52/Laos/2020.
- SimPlot++_groups for PCoV GD (PCoV_GD: PCoV_A22-2, PCoV_MP789, PCoV_SM44-9, PCoV_SM79-9) query plot, single genomes except for these groups: PCoV_GX: GX_P2V, PCoV_GX-P1E, PCoV_GX-P4L, PCoV_GX-P5E, PCoV_GX-P5L, BANAL: BANAL-20-103/Laos/2020, BANAL-20-116/Laos/2020, BANAL-20-236/Laos/2020, BANAL-20-236/Laos/2020, BANAL-20-247/Laos/2020, BANAL-20-52/Laos/2020.
3. Results
3.1. Mitochondrial Mapping Analysis
3.2. Identification of Human Mitochondrial Haplogroups
3.3. Simplot Analysis
3.4. Phylogenetic Analysis
3.5. Recombination Analysis
3.6. Synthetic Vectors
3.7. Human and Mouse Hosted Viruses
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Source Code
References
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Jones, A.; Massey, S.E.; Zhang, D.; Deigin, Y.; Quay, S.C. Forensic Analysis of Novel SARS2r-CoV Identified in Game Animal Datasets in China Shows Evolutionary Relationship to Pangolin GX CoV Clade and Apparent Genetic Experimentation. Appl. Microbiol. 2022, 2, 882-904. https://doi.org/10.3390/applmicrobiol2040068
Jones A, Massey SE, Zhang D, Deigin Y, Quay SC. Forensic Analysis of Novel SARS2r-CoV Identified in Game Animal Datasets in China Shows Evolutionary Relationship to Pangolin GX CoV Clade and Apparent Genetic Experimentation. Applied Microbiology. 2022; 2(4):882-904. https://doi.org/10.3390/applmicrobiol2040068
Chicago/Turabian StyleJones, Adrian, Steven E. Massey, Daoyu Zhang, Yuri Deigin, and Steven C. Quay. 2022. "Forensic Analysis of Novel SARS2r-CoV Identified in Game Animal Datasets in China Shows Evolutionary Relationship to Pangolin GX CoV Clade and Apparent Genetic Experimentation" Applied Microbiology 2, no. 4: 882-904. https://doi.org/10.3390/applmicrobiol2040068