Dynamics of natural selection preceding human viral epidemics and pandemics
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Abstract
Using a phylogenetic framework to characterize natural selection, we investigate the hypothesis that zoonotic viruses require adaptation prior to zoonosis to sustain human-to-human transmission. Examining the zoonotic emergence of Ebola virus, Marburg virus, influenza A virus, SARS-CoV, and SARS-CoV-2, we find no evidence of a change in the intensity of natural selection immediately prior to a host switch, compared with typical selection within reservoir hosts. We conclude that extensive pre-zoonotic adaptation is not necessary for human-to-human transmission of zoonotic viruses. In contrast, the reemergence of H1N1 influenza A virus in 1977 showed a change in selection, consistent with the hypothesis of passage in a laboratory setting prior to its reintroduction into the human population, purportedly during a vaccine trial. Holistic phylogenetic analysis of selection regimes can be used to detect evolutionary signals of host switching or laboratory passage, providing insight into the circumstances of past and future viral emergence.
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This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/15265995.
The authors investigated viral adaptation's necessity prior to successful zoonosis to sustain human-to-human transmission by examining pandemic causing viruses (Ebola virus, Marburg virus, influenza A virus, SARS-CoV, and SARS-CoV-2). Viral adaptation was measured as selection rate (ω) – purifying selection(ω < 1), diversifying selection(ω > 1) and neural selection (ω ~ 1). Genome-wide selection was then compared on three periods on the phylogenetic tree for the analysis: 1) viruses in their natural animal hosts (background); 2) during the transmission from animals to humans (stem); and 3) in the early stages of outbreaks in humans (outbreak). Authors found that by comparing with selection …
This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/15265995.
The authors investigated viral adaptation's necessity prior to successful zoonosis to sustain human-to-human transmission by examining pandemic causing viruses (Ebola virus, Marburg virus, influenza A virus, SARS-CoV, and SARS-CoV-2). Viral adaptation was measured as selection rate (ω) – purifying selection(ω < 1), diversifying selection(ω > 1) and neural selection (ω ~ 1). Genome-wide selection was then compared on three periods on the phylogenetic tree for the analysis: 1) viruses in their natural animal hosts (background); 2) during the transmission from animals to humans (stem); and 3) in the early stages of outbreaks in humans (outbreak). Authors found that by comparing with selection rates during background period, viruses don't have significant adaptation (selection rate) change during stem period but outbreak periods.
Overall, the manuscript is clear on their findings. However, it would improve the manuscript if the authors address the following points:
"we have extended the RELAX framework to account for multiple evolutionary histories in different genomic segments" An explanation on the implementation of such extension would be useful to facilitate understanding of the analysis results in the manuscript.
Three time periods for each virus were chosen differently rather uniformly. Although each outbreak could be different due to the virus's unique transmissibility, it would be useful to test out whether varying the length of each period would change the finding. This would verify the robustness of analysis conducted in the manuscript.
Competing interests
The author declares that they have no competing interests.
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