Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bioethics, Sample Collection and Processing
2.2. Whole-Genome Sequencing, Assembly, and Quality Control
2.3. Identification of Lineage Counterparts
2.4. Parental Lineages Determination
2.5. Network Analyses
2.6. Recombination Analyses
2.7. Phylogenetic Analyses
2.8. Estimating the Age of Introgression
3. Results
3.1. Sampling, Data Acquisition, and Genome Assembly
3.2. Identification of the Brazilian Deltacron, AYBA-RS
3.3. Comparison between AYBA-RS and the Other Deltacrons
3.4. Evolutionary History of Recombinants of VOC Delta and VOC Omicron
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Brazil/RS-315-66266-219/2022 | Brazil/SC2-9898/2022 | Brazil/RS-FIOCRUZ-8390/2022 | |
---|---|---|---|
Accession ID | EPI_ISL_14284846 | EPI_ISL_14381991 | EPI_ISL_13523515 |
Sample date | 6 June 2022 | 2 May 2022 | 12 February 2022 |
Location | Santa Maria | Porto Alegre | Cruz Alta |
Mapped reads | 514,768 | 602,459 | 3,039,386 |
Coverage breadth | >30 × 98.79% | >30 × 98.70% | >30 × 99% |
Coverage depth | 798× | 532× | 10,000× |
Library construction method | COVIDSeq Assay Illumina | PARAGON CleanPlex SARS-CoV-2 FLEX Panel | COVIDSeq Assay Illumina |
Sequencing technology | Illumina iSeq 100 | Illumina MiSeq | Illumina MiSeq |
Assembly method | ViralFlow | SOPHiA DDM v.5 | ViralFlow |
Sample (Lineage) | Segment Start | Segment End | Nextclade * | Pangolin # | Lineage of the Top-Hit (Strain Name) $ |
---|---|---|---|---|---|
Brazil/RS-FIOCRUZ-8390/2022 (AYBA-RS) | 37 | 21,845 | AY.101 | AY.101 | AY.100 (Guatemala/INC-LNS-127/2021) |
Brazil/RS-FIOCRUZ-8390/2022 (AYBA-RS) | 21,846 | 29,857 | BA.1 | - | BA.1.1 (Taiwan/TSGH-52/2021) |
France/HDF-IPP54794/2022 (XD) | 55 | 21,845 | XD | XD | BA.1 (Brazil/BA-FIOCRUZ-PVM99977/2022) |
France/HDF-IPP54794/2022 (XD) | 21,846 | 25,469 | XD | - | AY.4 (Belgium/ULG-17464/2021) |
USA/CO-CDC-FG-248528/2022 (XS) | 38 | 10,029 | XS | - | B.1.617.2 (Pakistan/UHSPK3-61/2021) |
USA/CO-CDC-FG-248528/2022 (XS) | 10,030 | 29,792 | XS | - | BA.1.1 (Paraguay/454211/2022) |
Recombinant | Breakpoint Start | Breakpoint End | Minor Parental Lineages | Major Parental Lineages | RDP (p-Value) | GENECONV (p-Value) | Maxchi (p-Value) | Chimaera (p-Value) | SiSscan (p-Value) |
---|---|---|---|---|---|---|---|---|---|
AYBA-RS | 22,675 | 29,392 | BA.1.1, BA.1, XF, XS | AY.4, AY.101, B.1.617.2 | 8.21 × 10−6 | 3.89 ×10−5 | 6.05 × 10−10 | 1.20 × 10−9 | 1.33 × 10−8 |
XD | 21,804 | 25,526 | BA.1.1, BA.1, XF, XS | AY.4, AY.101, B.1.617.2 | 1.76 × 10−8 | 5.11 × 10−9 | 1.33 × 10−9 | 6.12 × 10−10 | 2.45 × 10−7 |
XS | 29,652 | 9751 | AY.4, AY.101, B.1.617.2, XD | BA.1.1, BA.1 | 0.012 | 2.04 × 10−4 | 0.001 | 0.002 | NS |
Sequences | SNP Divergence | Mean Time (in Days) | Min Time (5% CI) | Max Time (95% CI) |
---|---|---|---|---|
CA–RJ | 19 | 180 | 120 | 255 |
SM–CA | 16 | 152 | 100 | 222 |
PA–CA | 14 | 134 | 84 | 200 |
SM–RJ | 13 | 125 | 78 | 190 |
PA–RJ | 11 | 107 | 63 | 168 |
PA–SM | 4 | 42 | 18 | 83 |
Position | CA | PA | RJ | SM |
---|---|---|---|---|
245 | C | C | C | T |
647 | A | G | A | A |
1348 | C | C | T | C |
3464 | T | C | C | C |
4057 | T | C | C | C |
7075 | T | C | C | C |
7081 | C | T | T | T |
14,183 | C | T | T | T |
16,238 | G | C | C | C |
17,407 | T | C | C | C |
20,062 | G | T | T | T |
21,752 | T | T | C | T |
21,846 | T | T | C | T |
22,419 | C | C | C | T |
22,599 | G | A | G | A |
22,673 | C | C | T | C |
22,688 | A | A | G | A |
22,775 | G | G | A | G |
22,786 | A | A | C | A |
22,792 | C | C | T | C |
22,882 | T | G | T | G |
25,000 | T | T | T | C |
25,482 | C | A | A | A |
25,704 | T | C | C | C |
27,864 | C | T | T | T |
Lineage | South Brazil | Non-South Brazil |
---|---|---|
AY.101 | 15.68% (2580) | 1.44% (1590) |
BA.1.1 | 16.08% (2646) | 8.45% (9344) |
Other lineages | 68.24% (11,228) | 90.11% (99,645) |
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Sant’Anna, F.H.; Finger Andreis, T.; Salvato, R.S.; Muterle Varela, A.P.; Comerlato, J.; Gregianini, T.S.; Barcellos, R.B.; de Souza Godinho, F.M.; Resende, P.C.; da Luz Wallau, G.; et al. Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil. Vaccines 2023, 11, 212. https://doi.org/10.3390/vaccines11020212
Sant’Anna FH, Finger Andreis T, Salvato RS, Muterle Varela AP, Comerlato J, Gregianini TS, Barcellos RB, de Souza Godinho FM, Resende PC, da Luz Wallau G, et al. Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil. Vaccines. 2023; 11(2):212. https://doi.org/10.3390/vaccines11020212
Chicago/Turabian StyleSant’Anna, Fernando Hayashi, Tiago Finger Andreis, Richard Steiner Salvato, Ana Paula Muterle Varela, Juliana Comerlato, Tatiana Schäffer Gregianini, Regina Bones Barcellos, Fernanda Marques de Souza Godinho, Paola Cristina Resende, Gabriel da Luz Wallau, and et al. 2023. "Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil" Vaccines 11, no. 2: 212. https://doi.org/10.3390/vaccines11020212