PHYLOSCANNER: inferring transmission from within-and between-host pathogen genetic diversity
A central feature of pathogen genomics is that different infectious particles (virions and
bacterial cells) within an infected individual may be genetically distinct, with patterns of …
bacterial cells) within an infected individual may be genetically distinct, with patterns of …
Cornering HIV: taking advantage of interactions between selective pressures
Adaptive immune responses, cellular restrictive factors and antiretroviral drugs, target
multiple regions in the Human Immunodeficiency Virus (HIV) proteome, imposing diverse …
multiple regions in the Human Immunodeficiency Virus (HIV) proteome, imposing diverse …
[HTML][HTML] A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses
Natural selection often acts on multiple traits simultaneously. For example, the virus HIV-1
faces pressure to evade host immunity while also preserving replicative fitness. While past …
faces pressure to evade host immunity while also preserving replicative fitness. While past …
Impact of host genetics on HIV disease progression and treatment: new conflicts on an ancient battleground
D Nolan, S Gaudieri, M John, S Mallal - Aids, 2004 - journals.lww.com
Research into the effects of host genetics on HIV disease susceptibility and progression, and
on the efficacy and toxicity of drug treatment, occupies a particular position in the landscape …
on the efficacy and toxicity of drug treatment, occupies a particular position in the landscape …
Estimating HLA disease associations using similarity trees
The human leukocyte antigen (HLA) is associated with many (infectious) disease outcomes.
These associations are perhaps best documented for HIV-1. For example, the HLA-B* 58: 01 …
These associations are perhaps best documented for HIV-1. For example, the HLA-B* 58: 01 …
Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence
It is widely believed that epidemics in new hosts diminish in virulence over time, with natural
selection favoring pathogens that cause minimal disease. However, a tradeoff frequently …
selection favoring pathogens that cause minimal disease. However, a tradeoff frequently …
Frequent toggling between alternative amino acids is driven by selection in HIV-1
Host immune responses against infectious pathogens exert strong selective pressures
favouring the emergence of escape mutations that prevent immune recognition. Escape …
favouring the emergence of escape mutations that prevent immune recognition. Escape …
The impact of HIV-1 within-host evolution on transmission dynamics
Highlights•HIV-1 within-host evolution is short-sighted and favours more virulent
viruses.•Systemic HIV-1 infection is mainly established by a single variant …
viruses.•Systemic HIV-1 infection is mainly established by a single variant …
Identifying recombination hot spots in the HIV-1 genome
ABSTRACT HIV-1 infection is characterized by the rapid generation of genetic diversity that
facilitates viral escape from immune selection and antiretroviral therapy. Despite …
facilitates viral escape from immune selection and antiretroviral therapy. Despite …
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection
MR Henn, CL Boutwell, P Charlebois… - PLoS …, 2012 - journals.plos.org
Deep sequencing technologies have the potential to transform the study of highly variable
viral pathogens by providing a rapid and cost-effective approach to sensitively characterize …
viral pathogens by providing a rapid and cost-effective approach to sensitively characterize …