Patterns of Recombination in Coronaviruses
Abstract
1. Introduction
2. Results
2.1. Recombination Inferences
2.2. Constrained vs. Unconstrained Same-Species Phylogenetic Trees
2.3. Constrained vs. Unconstrained Different-Species Phylogenetic Trees
2.4. Non-Synonymous Divergence (Ka)
2.5. Recombination and Selection
3. Discussion
4. Materials and Methods
4.1. Sequence Retrieval
4.2. Recombination Inferences
4.3. Phylogenetic Analysis
4.4. Non-Synonymous Rate (Ka) of Evolution
4.5. Statistical Analyses
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Method | Gene | Total RB | |||||||
---|---|---|---|---|---|---|---|---|---|
ORF1a | ORF1b | S | E | M | N | Accessory | |||
3SEQ | RB | 174 | 271 | 220 | 7 | 22 | 34 | 158 | 886 |
%RB | 19.64 | 30.59 | 24.83 | 0.79 | 2.48 | 3.84 | 17.83 | 0.82 | |
%RB/%Alignment size | 0.47 | 0.92 | 1.97 | 0.20 | 1.17 | 0.67 | 1.79 | - | |
Geneconv | RB | 379 | 314 | 129 | 8 | 41 | 50 | 237 | 1158 |
%RB | 32.73 | 27.12 | 11.14 | 0.69 | 3.54 | 4.32 | 20.47 | 1.08 | |
%RB/%Alignment size | 0.58 | 0.82 | 1.07 | 1.34 | 1.36 | 1.67 | 2.25 | - | |
RDP | RB | 40118 | 24086 | 11094 | 488 | 1788 | 9148 | 18140 | 104862 |
%RB | 38.26 | 22.97 | 10.58 | 0.47 | 1.71 | 8.72 | 17.30 | 97.46 | |
%RB/%Alignment size | 0.60 | 0.52 | 0.90 | 1.21 | 0.86 | 2.38 | 4.08 | - | |
Bootscan | RB | 116 | 105 | 123 | 7 | 12 | 14 | 313 | 690 |
%RB | 16.81 | 15.22 | 17.83 | 1.01 | 1.74 | 2.03 | 45.53 | 0.64 | |
%RB/%Alignment size | 0.25 | 0.45 | 0.96 | 1.40 | 0.45 | 0.51 | 5.40 | - | |
Total per gene | RB | 40787 | 24776 | 11566 | 510 | 1863 | 9246 | 18848 | 107596 |
%RB | 37.91 | 23.03 | 10.75 | 0.47 | 1.73 | 8.59 | 17.52 | - | |
%RB/%Alignment size | 0.47 | 0.68 | 1.23 | 1.04 | 0.96 | 1.31 | 3.38 | - |
Genomic Region | Intratypic | Intertypic | |||
---|---|---|---|---|---|
Observed/Expected | Average | Observed/Expected | Average | ||
ORF1a | ORF1a | 0.83 | 1.23 | 2.04 | 0.59 |
ORF1b | 2.02 | 1.35 | |||
S | 1.25 | 0.59 | |||
E | 0.64 | 0.00 | |||
M | 0.97 | 0.00 | |||
N | 2.03 | 0.00 | |||
Accessory | 0.83 | 0.12 | |||
ORF1b | ORF1b | 1.01 | 1.69 | 13.19 | 2.25 |
S | 2.49 | 0.22 | |||
E | 1.60 | 0.00 | |||
M | 1.18 | 0.00 | |||
N | 1.22 | 0.00 | |||
Accessory | 2.28 | 1.00 | |||
S | S | 5.05 | 3.31 | 8.07 | 1.70 |
E | 2.37 | 0.00 | |||
M | 4.72 | 0.00 | |||
N | 3.39 | 0.54 | |||
Accessory | 3.94 | 2.50 | |||
E | E | NA | 3.17 | 16.73 | 2.43 |
M | 7.91 | 1.95 | |||
N | 6.18 | 0.00 | |||
Accessory | 3.50 | 0.73 | |||
M | M | 0.34 | 3.64 | 2.38 | 2.04 |
N | 6.51 | 9.75 | |||
Accessory | 3.86 | 0.17 | |||
N | N | 1.95 | 3.61 | 3.80 | 2.03 |
Accessory | 3.98 | 0.15 | |||
Accessory | Accessory | 4.37 | 3.25 | 0.17 | 0.69 |
Gene | Statistically Significant Trees | Statistically Insignificant Trees | # of Converged Trees | Total |
ORF1a | 20 (95.24%) | 1 (4.76%) | 19 (85.71%) | 21 |
ORF1b | 18 (85.71%) | 3 (14.29%) | 21 (100%) | |
E | 13 (61.90%) | 8 (38,10%) | 21 (100%) | |
M | 19 (90.48%) | 2 (9.52%) | 20 (95.24%) | |
N | 17 (80.95%) | 4 (19.05%) | 21 (100%) | |
Whole Genome | 21 (100%) | 0 (0%) | 20 (95.24%) | |
Total | 108 (85.71%) | 18 (14.29%) | 122 (96.83%) | 126 |
Dataset | Genus | Number of Sequences |
---|---|---|
hCoV-229E | Alphacoronavirus | 152 |
HKU2 | Alphacoronavirus | 10 |
HKU10 | Alphacoronavirus | 25 |
hCoV-NL63 | Alphacoronavirus | 151 |
PEDV | Alphacoronavirus | 851 |
TGEV | Alphacoronavirus | 62 |
GCCDC1 | Betacoronavirus | 9 |
hCoV-HKU1 | Betacoronavirus | 63 |
HKU4 | Betacoronavirus | 10 |
HKU9 | Betacoronavirus | 10 |
MERS-CoV (animal hosts) | Betacoronavirus | 334 |
MERS-CoV (human host) | Betacoronavirus | 286 |
MERS-CoV-related | Betacoronavirus | 631 |
Murine-CoV | Betacoronavirus | 38 |
hCoV-OC43 | Betacoronavirus | 342 |
PHEV | Betacoronavirus | 18 |
SARS-CoV | Betacoronavirus | 13 |
SARS-CoV-2 | Betacoronavirus | 2794 |
SARS-CoV-related | Betacoronavirus | 276 |
HKU15 | Deltacoronavirus | 200 |
IBV | Gammacoronavirus | 667 |
37 species with fewer than eight sequences | - | 92 |
Total | - | 7034 |
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Soares, R.; Vieira, C.P.; Vieira, J. Patterns of Recombination in Coronaviruses. Int. J. Mol. Sci. 2025, 26, 5595. https://doi.org/10.3390/ijms26125595
Soares R, Vieira CP, Vieira J. Patterns of Recombination in Coronaviruses. International Journal of Molecular Sciences. 2025; 26(12):5595. https://doi.org/10.3390/ijms26125595
Chicago/Turabian StyleSoares, Ricardo, Cristina P. Vieira, and Jorge Vieira. 2025. "Patterns of Recombination in Coronaviruses" International Journal of Molecular Sciences 26, no. 12: 5595. https://doi.org/10.3390/ijms26125595
APA StyleSoares, R., Vieira, C. P., & Vieira, J. (2025). Patterns of Recombination in Coronaviruses. International Journal of Molecular Sciences, 26(12), 5595. https://doi.org/10.3390/ijms26125595