Single stranded RNA viruses like coronaviruses can recombine with each other. During the viral RNA replication, the viral polymerase can jump onto another template strand and result in a chimeric genomic RNA. why do RNA viruses recombine

However, trying to extrapolate this model to DNA viruses will encounter a big problem. Most DNA viruses have double stranded genomes. The replication of dsDNA is semiconservative, which means the template (parent DNA) is also a part of the daughter DNA. Even if the DNA polymerase jumps in the halfway, the template DNA won’t move with it. Does that mean DNA viruses don’t recombine, or recombine in different ways?


1 Answer 1


Certainly DNA viruses do recombine — some of them encode proteins specifically for this purpose. And this is unsurprising if one reflects on the fact that recombination is a fundamental characteristic of double-stranded genomic DNA in prokaryotes and eukaryotes. What is surprising is that recombination occurs in RNA viruses — the starting point for the question. However the mechanism by which this can occur — apparently in a random manner — is completely different from the long established way in which double-stranded DNA genomes recombine.

The literature on recombination is vast. For the purposes of an answer to this rather naive question, I think it sufficient to refer the reader to a Wikipedia article on recombination in general, and draw on a single review of recombination in DNA viruses.

Quoting from the aforementioned review by Weller and Sawitzke in Ann. Rev. Microbiology (2014) 68, pp 237–258:

“Homologous recombination plays many important roles in the biology of all living organisms including DNA replication and repair of DNA damage. Recombination is essential for genetic diversification required to enable organisms to adapt and evolve.“

The Wikipedia article deals first with ‘standard’ recombination in DNA genomes, which, although not identical in all situations, generally involves a double-strand break, pairing to a homologous region on another chromosome, and often ‘crossing-over” of the strands between the two chromosomes:

Crossing over

This is illustrated in more detail in the article, but one should emphasize that crossing-over involves an intermediate Holliday junction of four strands of DNA, as shown below for PDB file 1M6G.

Holliday junction

The idea that single-stranded nucleic acid is a requirement for the process (as assumed by the poster) is false.

Recombination is catalysed/promoted by specific proteins — recombinases — the most well-known being perhaps RecA in Escherichia coli and Rad5 in eukaryotes. Specific nucleases are also involved in making the strand breaks. What the review by Weller and Sawitzke focuses on is the evidence for similar recombination and recombinases (and nucleases) in DNA viruses as diverse as bacteriophage lambda and herpes simplex virus type 1. They examine the mechanism and identify the viral and host proteins involved and conclude that:

“Both bacteriophage λ and herpes simplex virus display high rates of recombination, both utilizing their own proteins and commandeering cellular proteins to promote recombination reactions.”


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