Genomic Context of SARS-CoV-2 Outbreaks in Farmed Mink in Spain during Pandemic: Unveiling Host Adaptation Mechanisms
Abstract
:1. Introduction
2. Results
2.1. Spanish Mink Sequences
2.2. Genomic Context
2.3. High Mutation Rate in Non-Structural Proteins
2.4. Spike Sequences Exhibit Host Adaptive Mutations
2.5. Mutations Detected in Mink Variants May Have the Potential to Trigger Spillover Events from Minks to Humans
3. Discussion
4. Materials and Methods
4.1. Sample Origin and Preparation
4.2. Virus Detection by RT-PCR
4.3. Sequencing Methods
4.4. Quality Control of the Sequences
4.5. Bioinformatics Analysis
4.6. Alignment and Phylogenetic Analysis
4.7. Protein Expression and Purification
4.8. Surface Plasmon Resonance (SPR) Assays
4.9. Structural Viewing
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Outbreak Number | Date of Notification to the National Level | Sample ID for Sequencing | Lineage | GISAID ID |
---|---|---|---|---|
1/2020 | 07/2020 | R.001630/20-091 | B.1 | EPI_ISL_19096372 |
R.001630/20-094 | B.1 | EPI_ISL_19096370 | ||
R.001630/20-103 | B.1 | EPI_ISL_19096341 | ||
R.001630/20-104 | B.1 | EPI_ISL_19096343 | ||
R.001630/20-115 | B.1 | EPI_ISL_19096354 | ||
R.001630/20-117 | B.1 | EPI_ISL_19096344 | ||
R.001630/20-124 | B.1 | EPI_ISL_19096345 | ||
R.001630/20-125 | B.1 | EPI_ISL_19096355 | ||
R.001630/20-126 | B.1 | EPI_ISL_19096356 | ||
R.001630/20-127 | B.1 | EPI_ISL_19096357 | ||
R.001630/20-137 | B.1 | EPI_ISL_19096358 | ||
R.001630/20-139 | B.1 | EPI_ISL_19096359 | ||
R.001630/20-141 | B.1 | EPI_ISL_19096360 | ||
R.001630/20-143 | B.1 | EPI_ISL_19096346 | ||
R.001630/20-144 | B.1 | EPI_ISL_19096347 | ||
R.001630/20-145 | B.1 | EPI_ISL_19096361 | ||
R.001630/20-146 | B.1 | EPI_ISL_19096362 | ||
R.001630/20-148 | B.1 | EPI_ISL_19096348 | ||
R.001630/20-150 | B.1 | EPI_ISL_19096363 | ||
R.001630/20-151 | B.1 | EPI_ISL_19096364 | ||
R.001630/20-152 | B.1 | EPI_ISL_19096365 | ||
R.001630/20-155 | B.1 | EPI_ISL_19096366 | ||
R.001630/20-157 | B.1 | EPI_ISL_19096367 | ||
R.001630/20-158 | B.1 | EPI_ISL_19096368 | ||
R.001630/20-161 | B.1 | EPI_ISL_19096369 | ||
R.001630/20-163 | B.1 | EPI_ISL_19096351 | ||
R.001630/20-167 | B.1 | EPI_ISL_19096350 | ||
R.001630/20-168 | B.1 | EPI_ISL_19096337 | ||
R.001630/20-169 | B.1 | EPI_ISL_19096352 | ||
R.001630/20-173 | B.1 | EPI_ISL_19096349 | ||
R.001630/20-175 | B.1 | EPI_ISL_19096340 | ||
R.001630/20-177 | B.1 | EPI_ISL_19096353 | ||
R.001630/20-178 | B.1 | EPI_ISL_19096339 | ||
R.001630/20-179 | B.1 | EPI_ISL_19096338 | ||
1/2021 | 21/01/2021 | R.004000/20-08 | B.1.177 | EPI_ISL_19096333 |
R.004000/20-15 | B.1.177 | EPI_ISL_19096334 | ||
R.004000/20-16 | B.1.177 | EPI_ISL_19096335 | ||
2/2021 | 25/01/2021 | R.000128/21-03 | B.1.177 | EPI_ISL_19096336 |
3/2021 | 17/03/2021 | R.000776/21-17 | B.1.177.50.1 | EPI_ISL_19096332 |
R.000776/21-18 | B.1.177 | EPI_ISL_19096331 | ||
R.000871/21-58 | B.1.177.50.1 | EPI_ISL_19096330 | ||
R.000871/21-62 | B.1.177.50.1 | EPI_ISL_19096329 | ||
R.000871/21-68 | B.1.177.50.1 | EPI_ISL_19096328 | ||
R.000871/21-97 | B.1.177 | EPI_ISL_19096326 | ||
R.000871/21-114 | B.1.177.50.1 | EPI_ISL_19096327 | ||
R.000871/21-116 | B.1.177.50.1 | EPI_ISL_19096325 | ||
R.001042/21-78 | B.1.177 | EPI_ISL_19096324 | ||
4/2021 | 09/06/2021 | R.001677/21-15 | B.1.1.7 | EPI_ISL_19096316 |
R.001677/21-52 | B.1.1.7 | EPI_ISL_19096315 | ||
R.001677/21-67 | B.1.1.7 | EPI_ISL_19096317 | ||
R.2207/21-3 | B.1.1.7 | EPI_ISL_19096312 | ||
R.2207/21-22 | B.1.1.7 | EPI_ISL_19096311 | ||
R.2207/21-36 | B.1.1.7 | EPI_ISL_19096309 | ||
R.2207/21-39 | B.1.1.7 | EPI_ISL_19096308 | ||
R.2207/21-46 | B.1.1.7 | EPI_ISL_19096307 | ||
R.0508/21-22 | B.1.1.7 | EPI_ISL_19096310 | ||
R.0508/21-58 | B.1.1.7 | EPI_ISL_19096306 | ||
R.1908/21-56 | B.1.1.7 | EPI_ISL_19096305 | ||
5/2021 | 25/06/2021 | R.001738/21-19 | B.1.1.7 | EPI_ISL_19096313 |
6/2021 | 25/06/2021 | R.001738/21-21 | B.1.1.7 | EPI_ISL_19096314 |
7/2021 | 25/06/2021 | R.001807/21-59 | B.1.1.7 | EPI_ISL_19096318 |
10/2021 | 19/07/2021 | R.002083/21-33 | B.1.1.7 | EPI_ISL_19096321 |
R.002366/21-27 | B.1.1.7 | EPI_ISL_19096322 | ||
R.002651/21-61 | B.1.617.2 | NA | ||
R.003234/21-26 | B.1.617.2 | NA | ||
11/2021 | 19/07/2021 | R.002026/21-100 | B.1.1.7 | EPI_ISL_19096319 |
R.002026/21-101 | B.1.1.7 | EPI_ISL_19096320 | ||
16/2021 | 11/10/2021 | R.002990/21-01 | AY.98.1 | EPI_ISL_19096323 |
17/2021 | 25/10/2021 | R.003064/21-01 | B.1.617.2 | NA |
R.003064/21-33 | B.1.617.2 | NA |
Mink Spikes | kon (1/Ms) × 105 | koff (1/s) × 10−2 | KD (nM) |
---|---|---|---|
Mink Cluster V | 0.91 ± 0.117 | 0.11 ± 0.009 | 12.3 ± 1.6 |
B.1 | 0.89 ± 0.041 | 0.92 ± 0.031 | 103.8 ± 8.3 |
B.1-N501T | 1.05 ± 0.008 | 0.25 ± 0.019 | 24.2 ± 1.6 |
B.1-F486L/N501T | 0.8 ± 0.007 | 0.94 ± 0.091 | 117.8 ± 10.6 |
B.1-F486V/N501T | 0.79 ± 0.02 | 0.69 ± 0.023 | 87.0 ± 5.1 |
B.1-VTH | 0.69 ± 0.027 | 0.79 ± 0.117 | 114.5 ± 12.4 |
B.1.177 | 0.89 ± 0.101 | 1.02 ± 0.042 | 114.4 ± 8.2 |
B.1.177-Y453F | 0.91 ± 0.008 | 0.1 ± 0.003 | 11.4 ± 0.5 |
B.1.1.7 | 1.6 ± 0.1 | 0.2 ± 0.019 | 12.3 ± 0.4 |
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© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
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Iglesias-Caballero, M.; Mas, V.; Vázquez-Morón, S.; Vázquez, M.; Camarero-Serrano, S.; Cano, O.; Palomo, C.; Ruano, M.J.; Cano-Gómez, C.; Infantes-Lorenzo, J.A.; et al. Genomic Context of SARS-CoV-2 Outbreaks in Farmed Mink in Spain during Pandemic: Unveiling Host Adaptation Mechanisms. Int. J. Mol. Sci. 2024, 25, 5499. https://doi.org/10.3390/ijms25105499
Iglesias-Caballero M, Mas V, Vázquez-Morón S, Vázquez M, Camarero-Serrano S, Cano O, Palomo C, Ruano MJ, Cano-Gómez C, Infantes-Lorenzo JA, et al. Genomic Context of SARS-CoV-2 Outbreaks in Farmed Mink in Spain during Pandemic: Unveiling Host Adaptation Mechanisms. International Journal of Molecular Sciences. 2024; 25(10):5499. https://doi.org/10.3390/ijms25105499
Chicago/Turabian StyleIglesias-Caballero, María, Vicente Mas, Sonia Vázquez-Morón, Mónica Vázquez, Sara Camarero-Serrano, Olga Cano, Concepción Palomo, María José Ruano, Cristina Cano-Gómez, José Antonio Infantes-Lorenzo, and et al. 2024. "Genomic Context of SARS-CoV-2 Outbreaks in Farmed Mink in Spain during Pandemic: Unveiling Host Adaptation Mechanisms" International Journal of Molecular Sciences 25, no. 10: 5499. https://doi.org/10.3390/ijms25105499