Section: Evolutionary Biology
Topic: Evolution, Health sciences, Genetics/Genomics

Convergent evolution as an indicator for selection during acute HIV-1 infection

Bertels, Frederic1  ; Metzner, Karin J.2 ; Regoes, Roland3 
1 Max Planck Institute for Evolutionary Biology - Plön, Germany
2 University Hospital Zurich, Division of Infectious Disease and Hospital Epidemiology - Zurich, Switzerland
3 Institut für Integrative Biologie, ETH Zurich - Zurich, Switzerland

Corresponding author(s): Bertels, Frederic ()

10.24072/pcjournal.6 - Peer Community Journal, Volume 1 (2021), article no. e4.

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Convergent evolution describes the process of different populations acquiring similar phenotypes or genotypes. Complex organisms with large genomes only rarely and only under very strong selection converge to the same genotype. In contrast, independent virus populations with very small genomes often acquire identical mutations. Here we test the hypothesis of whether convergence in early HIV-1 infection is common enough to serve as an indicator for selection. To this end, we measure the number of convergent mutations in a well-studied dataset of full-length HIV-1envgenes sampled from HIV-1 infected individuals during early infection. We compare this data to a neutral model and find an excess of convergent mutations. Convergent mutations are not evenly distributed across the env gene, but more likely to occur in gp41, which suggests that convergent mutations provide a selective advantage and hence are positively selected. In contrast, mutations that are only found in an HIV-1 population of a single individual are significantly affected by purifying selection. Our analysis suggests that comparisons between convergent and private mutations with neutral models allow us to identify positive and negative selection in small viral genomes. Our results also show that selection significantly shapes HIV-1 populations even before the onset of the adaptive immune system.
Published online:
DOI: 10.24072/pcjournal.6
Type: Research article

Bertels, Frederic 1; Metzner, Karin J. 2; Regoes, Roland 3

1 Max Planck Institute for Evolutionary Biology - Plön, Germany
2 University Hospital Zurich, Division of Infectious Disease and Hospital Epidemiology - Zurich, Switzerland
3 Institut für Integrative Biologie, ETH Zurich - Zurich, Switzerland
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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Bertels, Frederic; Metzner, Karin J.; Regoes, Roland. Convergent evolution as an indicator for selection during acute HIV-1 infection. Peer Community Journal, Volume 1 (2021), article  no. e4. doi : 10.24072/pcjournal.6. https://peercommunityjournal.org/articles/10.24072/pcjournal.6/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.evolbiol.100060

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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