The analysis of polymorphism data is becoming increasingly important as a complementary
tool to classical genetic analyses. Nevertheless, despite plunging sequencing costs …

Advances in sequencing technologies and increased access to sequencing services have
led to renewed interest in sequence and genome assembly. Concurrently, new applications …

Lymphoid tissue is a key reservoir established by HIV-1 during acute infection. It is a site
associated with viral production, storage of viral particles in immune complexes, and viral …

Advances in sequencing technologies have led to the increased use of high throughput
sequencing in characterizing the microbial communities associated with our bodies and our …

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 …

To dissect the mechanisms underlying the inflation of variants in the Severe Acute
Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) genome, we present a large-scale …

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) …

Genome sequencing technologies continue to develop with remarkable pace, yet analytical
approaches for reconstructing and classifying viral genomes from mixed samples remain …

A viral quasispecies, the ensemble of viral strains populating an infected person, can be
highly diverse. For optimal assessment of virulence, pathogenesis, and therapy selection …

Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission,
systemic infection is typically established by a limited number of founder viruses. Elucidation …