ArticleRetrovirology2017
Parent-offspring regression to estimate the heritability of an HIV-1 trait in a realistic setup.
Article in Retrovirology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Similar Changes in Proviral Landscapes Over 10 Years in 40 Individuals With Diverging HIV Reservoir Dynamics and Viral Load Kinetics.Open forum infectious diseases · 2026Article
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- The genetic architecture of HIV-1 virulence.Virus evolution · 2025Article
- Reconciling founder variant multiplicity of HIV-1 infection with the rate of CD4Journal of the Royal Society, Interface · 2024Article
- Self-reported neurocognitive complaints in the Swiss HIV Cohort Study: a viral genome-wide association study.Brain communications · 2024Article
- Absence of Proviral Human Immunodeficiency Virus (HIV) Type 1 Evolution in Early-Treated Individuals With HIV Switching to Dolutegravir Monotherapy During 48 Weeks.The Journal of infectious diseases · 2023Article
- Human Immunotypes Impose Selection on Viral Genotypes Through Viral Epitope Specificity.The Journal of infectious diseases · 2021Article
- Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART.Nature communications · 2020Article
- Article
- Inferring the age difference in HIV transmission pairs by applying phylogenetic methods on the HIV transmission network of the Swiss HIV Cohort Study.Virus evolution · 2018Article
- A Practical Guide to Estimating the Heritability of Pathogen Traits.Molecular biology and evolution · 2018Article
- Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity.Molecular biology and evolution · 2018Article
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Authors and funding
12 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundParent-offspring (PO) regression is a central tool to determine the heritability of phenotypic traits; i.e., the relative extent to which those traits are controlled by genetic factors. The applicability of PO regression to viral traits is unclear because the direction of viral transmission-who is the donor (parent) and who is the recipient (offspring)-is typically unknown and viral phylogenies are sparsely sampled.
methodsWe assessed the applicability of PO regression in a realistic setting using Ornstein-Uhlenbeck simulated data on phylogenies built from 11,442 Swiss HIV Cohort Study (SHCS) partial pol sequences and set-point viral load (SPVL) data from 3293 patients.
resultsWe found that the misidentification of donor and recipient plays a minor role in estimating heritability and showed that sparse sampling does not influence the mean heritability estimated by PO regression. A mixed-effect model approach yielded the same heritability as PO regression but could be extended to clusters of size greater than 2 and allowed for the correction of confounding effects. Finally, we used both methods to estimate SPVL heritability in the SHCS. We employed a wide range of transmission pair criteria to measure heritability and found a strong dependence of the heritability estimates to these criteria. For the most conservative genetic distance criteria, for which heritability estimates are conceptually expected to be closest to true heritability, we found estimates ranging from 32 to 46% across different bootstrap criteria. For less conservative distance criteria, we found estimates ranging down to 8%. All estimates did not change substantially after adjusting for host-demographic factors in the mixed-effect model (±2%).
conclusionsFor conservative transmission pair criteria, both PO regression and mixed-effect models are flexible and robust tools to estimate the contribution of viral genetic effects to viral traits under real-world settings. Overall, we find a strong effect of viral genetics on SPVL that is not confounded by host demographics.
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