Recombination and Positive Selection Differentially Shaped the Diversity of Betacoronavirus Subgenera.

Diego Forni,Manuela Sironi,Rachele Cagliani

doi:10.3390/v12111313

Abstract

The Betacoronavirus genus of mammal-infecting viruses includes three subgenera (Sarbecovirus, Embecovirus, and Merbecovirus), in which most known human coronaviruses, including SARS-CoV-2, cluster. Coronaviruses are prone to host shifts, with recombination and positive selection possibly contributing to their high zoonotic potential. We analyzed the role of these two forces in the evolution of viruses belonging to the Betacoronavirus genus. The results showed that recombination has been pervasive during sarbecovirus evolution, and it is more widespread in this subgenus compared to the other two. In both sarbecoviruses and merbecoviruses, recombination hotspots are clearly observed. Conversely, positive selection was a less prominent force in sarbecoviruses compared to embecoviruses and merbecoviruses and targeted distinct genomic regions in the three subgenera, with S being the major target in sarbecoviruses alone. Overall, the results herein indicate that Betacoronavirus subgenera evolved along different trajectories, which might recapitulate their host preferences or reflect the origins of the presently available coronavirus sequences.

Highlights

The members of the Coronaviridae family are enveloped, positive-sense, single-stranded RNA viruses infecting three classes of vertebrates: mammals, birds, and fish.Coronaviruses have long and complex genomes, unusual if compared to those of other RNA viruses.A large portion of the coronavirus genome encodes two large, overlapping open reading frames (ORF1a and ORF1b) that are translated and processed into 16 non-structural proteins [1]
In panel b, and HCoV-OC43 in reported for SARS-CoV-2 in panel a, MERS-CoV in panel b, and HCoV-OC43 in panel c. We evaluated whether these events had a major effect in the evolution of sarbecoviruses and if recombination occurs with similar frequencies in other Betacoronavirus subgenera
We analyzed the evolution of the genomes of viruses belonging to different Betacoronavirus subgenera with the aim of assessing the relative importance of two evolutionary forces, namely, recombination and positive selection

Summary

Introduction

The members of the Coronaviridae family (order Nidovirales) are enveloped, positive-sense, single-stranded RNA viruses infecting three classes of vertebrates: mammals, birds, and fish.Coronaviruses have long and complex genomes, unusual if compared to those of other RNA viruses.A large portion of the coronavirus genome encodes two large, overlapping open reading frames (ORF1a and ORF1b) that are translated and processed into 16 non-structural proteins (nsp to16) [1]. Coronaviruses have long and complex genomes, unusual if compared to those of other RNA viruses. A large portion of the coronavirus genome encodes two large, overlapping open reading frames (ORF1a and ORF1b) that are translated and processed into 16 non-structural proteins The remaining portion of the genome encodes structural proteins—spike (S), envelope (E), membrane (M), and nucleoprotein (N)—as well as a variable number of accessory proteins [1,2,3]. The recently emerged human-infecting coronavirus, referred to as SARS-CoV-2 [6] and responsible for the recent pandemic, clusters with SARS-CoV (severe acute respiratory syndrome coronavirus) and other bat-derived viruses in the Sarbecovirus subgenus [6,7,8]

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