RESUMEN
Current methods to detect intraclade HIV dual infection are poorly suited for determining its prevalence in large cohorts. To investigate the potential of ultra-deep sequencing to screen for dual infection, we compared it to bulk sequence-based synonymous mixture index and the current standard of single genome sequencing. The synonymous mixture index identified samples likely to harbor dual infection, while ultra-deep sequencing captured more intra-host viral diversity than single genome sequencing at approximately 40% of the cost and 20% of the laboratory and analysis time. The synonymous mixture index and ultra-deep sequencing are promising methods for rapid and cost-effective systematic identification of HIV dual infection.
Asunto(s)
Variación Genética , Infecciones por VIH/virología , VIH/clasificación , VIH/aislamiento & purificación , Virología/métodos , Adulto , Análisis por Conglomerados , VIH/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Masculino , Persona de Mediana Edad , Datos de Secuencia Molecular , Análisis de Secuencia de ADN , Homología de SecuenciaRESUMEN
Although it is known that most HIV-1 infections worldwide result from exposure to virus in semen, it has not yet been established whether transmitted strains originate as RNA virions in seminal plasma or as integrated proviral DNA in infected seminal leukocytes. We present phylogenetic evidence that among six transmitting pairs of men who have sex with men, blood plasma virus in the recipient is consistently more closely related to the seminal plasma virus in the source. All sequences were subtype B, and the env C2V3 of transmitted variants tended to have higher mean isoelectric points, contain potential N-linked glycosylation sites, and favor CCR5 co-receptor usage. A statistically robust phylogenetically corrected analysis did not detect genetic signatures reliably associated with transmission, but further investigation of larger samples of transmitting pairs holds promise for determining which structural and genetic features of viral genomes are associated with transmission.