Diagnostic and vaccination approaches for Newcastle disease virus in poultry: The current and emerging perspectives
Newcastle disease (ND) is one of the most devastating diseases that considerably cripple
the global poultry industry. Because of its enormous socioeconomic importance and …
the global poultry industry. Because of its enormous socioeconomic importance and …
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 …
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
The study of cell-population heterogeneity in a range of biological systems, from viruses to
bacterial isolates to tumor samples, has been transformed by recent advances in …
bacterial isolates to tumor samples, has been transformed by recent advances in …
De novo assembly of highly diverse viral populations
Background Extensive genetic diversity in viral populations within infected hosts and the
divergence of variants from existing reference genomes impede the analysis of deep viral …
divergence of variants from existing reference genomes impede the analysis of deep viral …
[HTML][HTML] High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance
Increasing globalization, agricultural intensification, urbanization, and climatic changes have
resulted in a significant recent increase in emerging infectious zoonotic diseases. Zoonotic …
resulted in a significant recent increase in emerging infectious zoonotic diseases. Zoonotic …
Vaccine-induced CD8+ T cells control AIDS virus replication
Develo** a vaccine for human immunodeficiency virus (HIV) may be aided by a complete
understanding of those rare cases in which some HIV-infected individuals control replication …
understanding of those rare cases in which some HIV-infected individuals control replication …
Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations
Next-generation sequencing (NGS) technologies enable new insights into the diversity of
virus populations within their hosts. Diversity estimation is currently restricted to single …
virus populations within their hosts. Diversity estimation is currently restricted to single …
Next-generation sequencing for HIV drug resistance testing: laboratory, clinical, and implementation considerations
Higher accessibility and decreasing costs of next generation sequencing (NGS), availability
of commercial kits, and development of dedicated analysis pipelines, have allowed an …
of commercial kits, and development of dedicated analysis pipelines, have allowed an …
[HTML][HTML] Recent advances in inferring viral diversity from high-throughput sequencing data
Rapidly evolving RNA viruses prevail within a host as a collection of closely related variants,
referred to as viral quasispecies. Advances in high-throughput sequencing (HTS) …
referred to as viral quasispecies. Advances in high-throughput sequencing (HTS) …
Measurements of intrahost viral diversity are extremely sensitive to systematic errors in variant calling
With next-generation sequencing technologies, it is now feasible to efficiently sequence
patient-derived virus populations at a depth of coverage sufficient to detect rare variants …
patient-derived virus populations at a depth of coverage sufficient to detect rare variants …