title: Identification of HIV superinfection in seroconcordant couples in Rakai, Uganda, by use of next-generation deep sequencing.
abstract: HIV superinfection, which occurs when a previously infected individual acquires a new distinct HIV strain, has been described in a number of populations. Previous methods to detect superinfection have involved a combination of labor-intensive assays with various rates of success. We designed and tested a next-generation sequencing (NGS) protocol to identify HIV superinfection by targeting two regions of the HIV viral genome, p24 and gp41. The method was validated by mixing control samples infected with HIV subtype A or D at different ratios to determine the inter- and intrasubtype sensitivity by NGS. This amplicon-based NGS protocol was able to consistently identify distinct intersubtype strains at ratios of 1% and intrasubtype variants at ratios of 5%. By using stored samples from the Rakai Community Cohort Study (RCCS) in Uganda, 11 individuals who were HIV seroconcordant but virally unlinked from their spouses were then tested by this method to detect superinfection between 2002 and 2005. Two female cases of HIV intersubtype superinfection (18.2%) were identified. These results are consistent with other African studies and support the hypothesis that HIV superinfection occurs at a relatively high rate. Our results indicate that NGS can be used for detection of HIV superinfection within large cohorts, which could assist in determining the incidence and the epidemiologic, virologic, and immunological correlates of this phenomenon.
authors.affiliation: Johns Hopkins University School of Medicine, Rangos Building, Room 530, 855 N Wolfe St, Baltimore, MD 21205, USA.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Redd
authors.forename: Aleisha
authors.initials: A
authors.lastname: Collinson-Streng
authors.forename: Craig
authors.initials: C
authors.lastname: Martens
authors.forename: Stacy
authors.initials: S
authors.lastname: Ricklefs
authors.forename: Caroline E
authors.initials: CE
authors.lastname: Mullis
authors.forename: Jordyn
authors.initials: J
authors.lastname: Manucci
authors.forename: Aaron A R
authors.initials: AA
authors.lastname: Tobian
authors.forename: Ethan J
authors.initials: EJ
authors.lastname: Selig
authors.forename: Oliver
authors.initials: O
authors.lastname: Laeyendecker
authors.forename: Nelson
authors.initials: N
authors.lastname: Sewankambo
authors.forename: Ronald H
authors.initials: RH
authors.lastname: Gray
authors.forename: David
authors.initials: D
authors.lastname: Serwadda
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Wawer
authors.forename: Stephen F
authors.initials: SF
authors.lastname: Porcella
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Quinn
mesh_terms: D000293:Adolescent; D000328:Adult; D015331:Cohort Studies; D005191:Family Characteristics; D005260:Female; D006678:HIV / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D016655:HIV Core Protein p24 / Q000235:genetics; D015700:HIV Envelope Protein gp41 / Q000235:genetics; D015658:HIV Infections / Q000175:diagnosis*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D014454:Uganda; D055815:Young Adult
chemical_list: D016655:HIV Core Protein p24; D015700:HIV Envelope Protein gp41