Related Experiment Video
Updated: Sep 1, 2025

Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization
Published on: December 23, 2020
Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape
Yatish Turakhia1,2,3, Bryan Thornlow4,5, Angie Hinrichs5
1Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA. yturakhia@ucsd.edu.
Abstract:
Accurate and timely detection of recombinant lineages is crucial for interpreting genetic variation, reconstructing epidemic spread, identifying selection and variants of interest, and accurately performing phylogenetic analyses1-4. During the SARS-CoV-2 pandemic, genomic data generation has exceeded the capacities of existing analysis platforms, thereby crippling real-time analysis of viral evolution5. Here, we use a new phylogenomic method to search a nearly comprehensive SARS-CoV-2 phylogeny for recombinant lineages. In a 1.6 million sample tree from May 2021, we identify 589 recombination events, which indicate that around 2.7% of sequenced SARS-CoV-2 genomes have detectable recombinant ancestry. Recombination breakpoints are inferred to occur disproportionately in the 3' portion of the genome that contains the spike protein. Our results highlight the need for timely analyses of recombination for pinpointing the emergence of recombinant lineages with the potential to increase transmissibility or virulence of the virus. We anticipate that this approach will empower comprehensive real-time tracking of viral recombination during the SARS-CoV-2 pandemic and beyond.
More Related Videos
Related Concept Videos
Viral Recombination
Evolutionary Relationships through Genome Comparisons
Conservative Site-specific Recombination and Phase Variation
The recognition sites for Cre recombinase called LoxP...
Single Nucleotide Polymorphisms-SNPs
Horizontal Gene Transfer
Gene Duplication and Divergence
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...

