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Viral Recombination

Viral Recombination

Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.

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Updated: Jul 17, 2025

Production of a SARS-CoV-2 Virus-Like-Particle System to Investigate Viral Life Cycles In Vitro

Production of a SARS-CoV-2 Virus-Like-Particle System to Investigate Viral Life Cycles In Vitro

Published on: June 6, 2025

Tracking and curating putative SARS-CoV-2 recombinants with RIVET.

Kyle Smith¹, Cheng Ye², Yatish Turakhia²

¹Department of Biological Sciences, University of California, San Diego, San Diego, CA 92093, United States.

Bioinformatics (Oxford, England)

|August 31, 2023

Summary

Identifying SARS-CoV-2 recombinants is challenging. RIVET is a new software pipeline that accelerates the detection and tracking of these viral strains, improving our understanding of virus evolution and spread.

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Last Updated: Jul 17, 2025

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Area of Science:

Virology
Computational Biology
Genomics

Background:

Accurate identification and tracking of SARS-CoV-2 recombinant strains are crucial for understanding viral evolution and controlling pandemics.
The rapid influx of daily genome sequences presents significant challenges for timely and confident recombinant identification, leading to delays in public health response.

Purpose of the Study:

To develop and present RIVET, a software pipeline and visual platform designed to comprehensively and sensitively detect potential SARS-CoV-2 recombinants.
To accelerate the identification and tracking of SARS-CoV-2 recombinants through an integrated web interface.

Main Methods:

RIVET leverages recent algorithmic advancements in recombination inference.
The pipeline processes large volumes of SARS-CoV-2 genome sequences.
A web interface organizes and presents analysis results for potential recombinants.

Main Results:

RIVET offers a sensitive and comprehensive approach to identifying SARS-CoV-2 recombinants.
The associated web interface provides up-to-date analysis of potential recombinants.
The RIVET pipeline significantly accelerates the detection and tracking process.

Conclusions:

RIVET enhances the ability to monitor SARS-CoV-2 evolution by enabling rapid identification of recombinant strains.
The platform facilitates a more effective response to the spread of SARS-CoV-2 by reducing delays in recombinant detection.