Studies suggest a possible increase in SARS-CoV-2 recombinants in the future

A recent amazing feat by U.S. researchers has revealed that recombination is not just widespread in evolutionary history like SARS. Coronavirus, But it can also enhance the fitness characteristics of seasonal coronaviruses. Their treatise is now bioRxiv* A preprint server that sets the stage for phylogenetic tracking of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Since its advent, gene sequence data has been used to study the evolution and spread of SARS-CoV-2, the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. As a result, the research community quickly adopted phylogenetic and phylogenetic techniques as an essential tool for studying this RNA virus.

In addition to mutations caused by errors during the replication process, various recombination processes can contribute to the genetic diversity of RNA viruses. In addition, reassortment of segmented viruses (such as rotavirus and influenza virus) can result in offspring harboring segments from different parental strains.

In any case, recombination always challenges phylogenetic methods because it violates the central assumption that the evolutionary history of an individual can be represented by the branching of the phylogenetic tree. As a result, recombination requires a shared ancestral representation of the set of sequences as a network.

In this study, Dr. Nikola Felix Müller, Dr. Kathryn E. Kistler, and Dr. Trevor Bedford of the Fred Hutchinson Cancer Research Center and the University of Washington, Seattle (USA) collaborated on the Markov Chain Monte Carlo approach to efficiently infer recombination. Was developed. Network from gene sequence data under a recombinant template switching model.

History of the evolution of SARS-like viruses. Maximum clade reliability network for viruses like SARS. Blue dots indicate samples and green dots indicate rejoin events. B Wuhan-Hu1 (SARS-CoV-2) has a common ancestral time and different SARS-like viruses at different locations in the genome. The y-axis shows the common ancestor time on a logarithmic scale. The latest time on the genome that C Wuhan-Hu1 shared a common ancestor with different SARS-like viruses

Evaluation of recombination pattern

Researchers have reconstructed the history of recombination of SARS-like viruses, including the original SARS-CoV-1 and the new SARS-CoV-2, and associated bat and pangoline coronaviruses. Next, they investigated examples of different viruses finally sharing a common ancestor along the genome.

The recombination pattern was further evaluated for Middle East respiratory syndrome coronavirus (MERS-CoV) and more than 2,500 cases were identified in humans. In addition, the human seasonal coronavirus OC43, 229E, and NL63 show a broad seasonal cycle.

They then sought to see if recombination rates increased in parts of the genome that also showed strong signs of adaptation. This was done by calculating the adaptation rates of seasonal human coronaviruses in different parts of the genome.

In short, such an approach and this type of framework have enabled a combination of recombinant networks, velocities, and effective population estimates, but also parameters that depict mutations over time from sampled sequence data. Made possible.

SARS-like history of complex evolution of coronavirus

This paper clearly shows that recombination events are widespread in the evolutionary history of SARS-like coronaviruses, and that the recombination rates of the aforementioned human seasonal coronaviruses tend to vary with adaptation. I will. This means that recombination may be beneficial to the fitness of human seasonal coronavirus.

On the other hand, the evolutionary history of coronaviruses such as SARS has been shown to be very complex and much less similar to tree-like evolution. In addition, researchers have shown that in the recent history of SARS-CoV-2, recombination has only been seen among closely related SARS-like viruses.

One notable finding was that recombination habitually occurs in human coronaviruses at rates comparable to influenza virus reassortment. Recombinant breakpoints in human coronavirus can also change depending on the rate of adaptation of the entire genome. This suggests that recombination events are selected positively or negatively based on the tendency for such breakpoints to occur.

An example of a recombinant network. Events that can occur in the rejoined network, as discussed here. We consider events to occur retroactively from the present (the standard when looking at the coalescing process. They occur at predefined times and you can add lineages when sampling conditional events. Rejoining events are Split the path of two strains, where all on one side of the recombination breakpoint goes to one side and everything on the other side of the breakpoint goes in the opposite direction.

Phylogenetic reconstruction

Knowing the extent to which recombination is expected to form SARS-CoV-2 in the next few years, identifying such events, and having the tools to perform phylogenetic reconstruction is our diagnostic weapon. Obviously, it will be an essential addition to the warehouse.

“Estimating the harmful loading of the virus before and after recombination using ancestral sequence remodeling may help clarify which sequences are preferred during recombination,” he said. The author of the study states bioRxiv paper.

“In addition, seasonal coronaviruses should reveal the role that recombination plays in the long-term evolution of these viruses, as there are additional sequences to reconstruct the recombination pattern,” they conclude. It is attached.

A plausible rise in SARS-CoV-2 recombinants in the future will increase the need for methods of performing phylogenetic and phylogenetic reasoning in the presence of recombination. Finally, the applicability of recombinant models will open the door to more widespread use of models for studying the spread of pathogens.

*Important Notices

bioRxiv Publish preliminary scientific reports that should not be considered definitive as they are not peer-reviewed, guide clinical practice / health-related behaviors, and should not be treated as established information.