Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data
Many viruses, including the clinically relevant RNA viruses HIV (human immunodeficiency
virus) and HCV (hepatitis C virus), exist in large populations and display high genetic …
virus) and HCV (hepatitis C virus), exist in large populations and display high genetic …
New virologic tools for management of chronic hepatitis B and C
S Chevaliez, C Rodriguez, JM Pawlotsky - Gastroenterology, 2012 - Elsevier
Molecular biology techniques are routinely used to diagnose and monitor treatment of
patients with chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infections. These …
patients with chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infections. These …
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 …
Prevalence of epistasis in the evolution of influenza A surface proteins
The surface proteins of human influenza A viruses experience positive selection to escape
both human immunity and, more recently, antiviral drug treatments. In bacteria and viruses …
both human immunity and, more recently, antiviral drug treatments. In bacteria and viruses …
The evolution of HIV: inferences using phylogenetics
Molecular phylogenetics has revolutionized the study of not only evolution but also disparate
fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular …
fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular …
HIV-1 adaptation to HLA: a window into virus–host immune interactions
HIV-1 develops specific mutations within its genome that allow it to escape detection by
human leukocyte antigen (HLA) class I-restricted immune responses, notably those of CD8+ …
human leukocyte antigen (HLA) class I-restricted immune responses, notably those of CD8+ …
Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA
W Shao, VF Boltz, JE Spindler, MF Kearney… - Retrovirology, 2013 - Springer
Background 454 sequencing technology is a promising approach for characterizing HIV-1
populations and for identifying low frequency mutations. The utility of 454 technology for …
populations and for identifying low frequency mutations. The utility of 454 technology for …
Epidemiological and clinical consequences of within-host evolution
Many viruses and bacteria are known to evolve rapidly over the course of an infection.
However, epidemiological studies generally assume that within-host evolution is an …
However, epidemiological studies generally assume that within-host evolution is an …
Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection
R Batorsky, MF Kearney, SE Palmer… - Proceedings of the …, 2011 - National Acad Sciences
HIV adaptation to a host in chronic infection is simulated by means of a Monte-Carlo
algorithm that includes the evolutionary factors of mutation, positive selection with varying …
algorithm that includes the evolutionary factors of mutation, positive selection with varying …
Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants
Reports of a high frequency of the transmission of minority viral populations with drug-
resistant mutations (DRM) are inconsistent with evidence that HIV-1 infections usually arise …
resistant mutations (DRM) are inconsistent with evidence that HIV-1 infections usually arise …