Kiki’s Comments                                                                                                        May 2020

            TWiV 619: Recombination led to emergence of SARS-CoV-2

            Key Points:

*book on COVID-19 in pre-print and available on Amazon—the pre-print version of the book is very alive as more information comes out

*the virus likely evolved in nature

*there are coronavirus peak zones of recombination, one of the most important recombination events in CoV-2 occurred in the spike

            Notes from the Raoul:

*Recombination analysis with SARS-CoV-2 genomes: we take the genomes and see where the information flow is happening. For non-recombining organisms, we have a decent idea of the phylogenetic structure that is much like a tree. When there is recombination, the structure is much more complex with part of the genome coming from one parent and part from another. For CoV-2 we have to see where all the different parts of the genome come from. We see very often that a single viral genome has multiple parental strains. The viruses evolve in two ways: 1)  mutations (usually frequency of mutation rate), 2) recombination (the mixing of different genomes). In beta coronaviruses, we saw that recombinations occurred throughout the genome, although with some hot spots that had a higher frequency of recombination.

*Recombination differences between SARS-CoV and SARS-CoV-2: Coronaviruses recombine a lot. There is an enrichment of the spike that is a major differentiator between CoV and CoV-2. There have been many recombinations, but there has been an important recombination in the spike region and others that have refined the mutations. There are many hypotheses to where these recombination events occurred, but it is likely that many of these occurred in bats.

*Furin cleavage site: evidence points to the fact that this mutation can occur in nature—supporting the evidence that SARS-CoV-2 evolved in nature

By Kiki Warren (