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With recombination I mean long ones, say > 1000 nucleotides, so that the two parents must be coronaviruses and the two pieces of genomes must have compatible genomic coordinates for the recombinant to be viable.

Though co-infection by distant CoVs (for example SARS-related with HKU2-related) are often found in nature, most recombinations occur between closely related coronaviruses. One thing preventing distant recombination is the TRS (a small motif causing most sub-genomic mRNA junctions) which must be compatible when the 5' part of an ORF is included in the transferred piece of genome. Another one is the complicated interactions between the host and viral proteins and RNA.

However, some rare distant recombinations might occur.

  • An example is Deltacoronavirus which is a distant genus except in the spike where it falls into Alphacoronavirus (though a bit distant to others).

  • There are also two Alphacoronaviruses: HKU2 (a normal one) and Wencheng shrew CoV (a distant one) that form a separate "genus" in the spike.

  • Swine enteric coronavirus (SeCoV) is a near perfect recombinant between two distant alphacoronaviruses, PEDV and TGEV (both responsible of enteric swine diseases).enter image description here

Are there other examples of recombination between distant Coronaviruses? Note that I mentioned one proven and three putatives recombinations, ie. we often don't have the triplet [major parent, minor parent, recombinant] as it is the case with SeCoV.

Discussing related lab experiments might be interesting as well (of note replacing VSV's G protein by various attachment&fusion proteins often produce viable chimera).

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  • $\begingroup$ In every case recombinations are rare as not many were found in the 2 million SARS-CoV-2 sequences, but they end being common when looking at the long-term evolutionary history of a given lineage. $\endgroup$
    – reuns
    Jul 17, 2021 at 12:47
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    $\begingroup$ Recombination between distant viruses is less likely to produce a viable virus, which is why is rarely observed (recombination rate in a cell may be nearly as high as for similar viruses). $\endgroup$
    – Roger V.
    Aug 14, 2021 at 5:23

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