Publication: Host ecosystems and viral quasispecies

Published: January 13th, 2013

Category: All News, Announcements, Bioinformatics, Latest Publications

This recent publication by lead author Dr. Li Yin, Department of Pathology, Immunology and Laboratory Medicine, describes the power of deep sequencing for understanding the dynamic nature of HIV-1 genetic diversity within infected individuals.

The study reveals the ebb and flow of dominant and rare viral variants, and identifies an evolutionary record of low-frequency cell-associated viral variants that persist for years in host environments. Dr. Maureen Goodenow is the senior author of the study.

Former ICBR Bioinformatics division scientists Li Liu and Yijun Sun developed several computational methods for analyzing the large collection of viral sequence data generated for the current study. These same computational methods can be applied to studying virome biodiversity in other biological systems.


Yin L, Liu L, Sun Y, Hou W, Lowe AC, Gardner BP, Salemi M, Williams WB, Farmerie WG, Sleasman JW, Goodenow MM. (2012). High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. Retrovirology, 9, 108.



Deep sequencing provides the basis for analysis of biodiversity of taxonomically similar organisms in an environment. While extensively applied to microbiome studies, population genetics studies of viruses are limited. To define the scope of HIV-1 population biodiversity within infected individuals, a suite of phylogenetic and population genetic algorithms was applied to HIV-1 envelope hypervariable domain 3 (Env V3) within peripheral blood mononuclear cells from a group of perinatally HIV-1 subtype B infected, therapy-naïve children.


Biodiversity of HIV-1 Env V3 quasispecies ranged from about 70 to 270 unique sequence clusters across individuals. Viral population structure was organized into a limited number of clusters that included the dominant variants combined with multiple clusters of low frequency variants. Next generation viral quasispecies evolved from low frequency variants at earlier time points through multiple non-synonymous changes in lineages within the evolutionary landscape. Minor V3 variants detected as long as four years after infection co-localized in phylogenetic reconstructions with early transmitting viruses or with subsequent plasma virus circulating two years later.


Deep sequencing defines HIV-1 population complexity and structure, reveals the ebb and flow of dominant and rare viral variants in the host ecosystem, and identifies an evolutionary record of low-frequency cell-associated viral V3 variants that persist for years. Bioinformatics pipeline developed for HIV-1 can be applied for biodiversity studies of virome populations in human, animal, or plant ecosystems.

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