Convergent evolution as an indicator for selection during acute HIV-1 infection
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...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Peer Community In
2021-11-01
|
| Series: | Peer Community Journal |
| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.6/ |
| _version_ | 1797651153985470464 |
|---|---|
| author | Bertels, Frederic Metzner, Karin J. Regoes, Roland |
| author_facet | Bertels, Frederic Metzner, Karin J. Regoes, Roland |
| author_sort | Bertels, Frederic |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T16:10:50Z |
| format | Article |
| id | doaj.art-0538516cf47a4caca366cbce16d6eca4 |
| institution | Directory Open Access Journal |
| issn | 2804-3871 |
| language | English |
| last_indexed | 2024-03-11T16:10:50Z |
| publishDate | 2021-11-01 |
| publisher | Peer Community In |
| record_format | Article |
| series | Peer Community Journal |
| spelling | doaj.art-0538516cf47a4caca366cbce16d6eca42023-10-24T14:38:25ZengPeer Community InPeer Community Journal2804-38712021-11-01110.24072/pcjournal.610.24072/pcjournal.6Convergent evolution as an indicator for selection during acute HIV-1 infectionBertels, Frederic0https://orcid.org/0000-0001-6222-4139Metzner, Karin J.1https://orcid.org/0000-0003-4862-1503Regoes, Roland2https://orcid.org/0000-0001-8319-5293Max Planck Institute for Evolutionary Biology - Plön, GermanyUniversity Hospital Zurich, Division of Infectious Disease and Hospital Epidemiology - Zurich, SwitzerlandInstitut für Integrative Biologie, ETH Zurich - Zurich, SwitzerlandConvergent 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.https://peercommunityjournal.org/articles/10.24072/pcjournal.6/ |
| spellingShingle | Bertels, Frederic Metzner, Karin J. Regoes, Roland Convergent evolution as an indicator for selection during acute HIV-1 infection Peer Community Journal |
| title | Convergent evolution as an indicator for selection during acute HIV-1 infection |
| title_full | Convergent evolution as an indicator for selection during acute HIV-1 infection |
| title_fullStr | Convergent evolution as an indicator for selection during acute HIV-1 infection |
| title_full_unstemmed | Convergent evolution as an indicator for selection during acute HIV-1 infection |
| title_short | Convergent evolution as an indicator for selection during acute HIV-1 infection |
| title_sort | convergent evolution as an indicator for selection during acute hiv 1 infection |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.6/ |
| work_keys_str_mv | AT bertelsfrederic convergentevolutionasanindicatorforselectionduringacutehiv1infection AT metznerkarinj convergentevolutionasanindicatorforselectionduringacutehiv1infection AT regoesroland convergentevolutionasanindicatorforselectionduringacutehiv1infection |