Author Interview: Most downloaded paper in October 2020

PeerJ talked to Alejandro Berrio Escobar about his recently published article “Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function”. This was PeerJ’s most downloaded article in October 2020.

Can you tell us a bit about yourself?

I am originally from Colombia and did my PhD at the University of Texas at Austin studying the evolution of monogamy and sexual fidelity in prairie voles. As a postdoc at Duke, I have been investigating the evolution of gene regulation in primates and sea urchins. Here, we developed and improved a method called adaptiPhy that can be used to detect regions of a genome with an excess of mutations relative to the rest of the genome. I am also interested in woodcarving, photography and flyfishing.

Can you briefly explain the research you published in PeerJ?

We implemented our method to investigate what regions of the genome make SARS-CoV-2 different from other coronaviruses. And, as expected, we found strong signals of divergence or positive selection in the gene that encodes Spike. The region that binds to ACE2 receptor showed significant changes earlier during its evolution. But we also found a signal in two other genes that encode for Nsp4 and Nsp16. These two genes are important for modifying membranes in the infected cell and avoiding the cell’s immune system. Moreover, we found that the sequence and 3D structure of the proteins they encode didn’t change with respect to closely related viruses, the coronavirus infecting bats (RaTG13) and Pangolins from Guangdong-China. Together, our results suggest that the changes that occurred in the SARS-CoV-2 genome may alter the structure of the RNA in a way that affects viral replication. Our work offers some insight into the changes that occurred during the life cycle of the coronavirus and can offer novel therapeutic targets.

Do you have any anecdotes about this research?

In February 2020 we didn’t understand this new virus, and at the time it seemed very dark and mysterious. So we decided to use the tools we have to shed some light, but we didn’t have any funding. Despite not having any money, we were able to invest our times and expertise to bring a little bit of light into the knowledge of the novel coronavirus.

What kinds of lessons do you hope your readers take away from the research?

I hope readers will have a better understanding of what changes occurred during the evolution of the coronavirus that favor its jump from non-human species to us. But there are also many questions and mysteries to solve. For example, how different are the RNA structures of SARS-CoV-2 to its closer relatives? What are the biological implications of those changes?

How did you first hear about PeerJ, and what persuaded you to submit to us?

We learned that the Duke library has a program that covers the publishing costs for journals that take Open Access seriously. And knowing that PeerJ has a great reputation in multiple fields, the decision wasn’t hard.

Do you have any comments about your overall experience with us?

During the peer review process, the editor and reviewers provided great constructive criticism that really helped improve our research. Also, it was the fastest, kindest, and most transparent that I have ever experienced.

How would you describe your experience of our submission/review process?

It was excellent.

Would you submit again, and would you recommend that your colleagues submit?

Absolutely!

You can find more PeerJ author interviews here. View related research in PeerJ’s Coronaviruses and Viral Respiratory Infections collection.