Figure 1: HIV-1 sequencing and linkage results for transmission
pairs. 3 Month Seroconverters were not included as study endpoints,
as seroconversion occurred prior to partners receipt of study drug.
Red circles emanating from Linked Gag boxes show the number of
linkages gained by gag sequencing. Determination of HIV
transmission linkage in the Partners in Prevention StudyMary S.
Campbell1, James I. Mullins1,2, James P. Hughes3, Kim G. Wong2,
Dana N. Raugi2, Stefanie Sorensen2, Julia N. Stoddard2, Hong Zhao2,
Wenjie Deng2, Francine E. McCutchan6, Jan Albert4, Thomas Leitner5,
Connie Celum1,7, Jairam R. Lingappa1,7,8Departments of Medicine1,
Microbiology2, Global Health7, and Pediatrics8, University of
Washington School of Medicine, Seattle, WA, USA, 3 University of
Washington School of Public Health and Community Medicine and the
Statistical Center for HIV/AIDS Research and Prevention, Seattle,
WA, USA, 4 Karolinska Institute and Swedish Institute for
Infectious Disease Control, Solna, Sweden, 5 Los Alamos National
Laboratory, Los Alamos, NM, USA, 6 Bill & Melinda Gates
Foundation, Seattle, WA, USAIAS 2009-LBPEC07UNIVERSITY OF
WASHINGTONINTERNATIONAL CLINICAL RESEARCH CENTERBackground-
Partners in Prevention Study: Randomized trial to evaluate genital
herpes suppression with acyclovir in HIV-1/HSV-2 infected
participants to prevent HIV-1 transmission to their partners1, 2-
Primary study endpoint: HIV-1 seroconversion (SC), in which the
HIV-1 strain acquired by the seroconverting partner was genetically
linked to his/her enrolled partnerMethods- HIV-1 viral RNA
extracted from plasma of index and seroconverter collected at or
within 3 months of SC- cDNA synthesized and PCR amplified partial
env (C2-C3-V3) and gag genes (p17/p24) - Consensus followed by
single molecule (SM) dideoxy terminator sequencing or
pyrosequencing, if viruses not found to be linked by consensus
sequencing- Sequence quality control, viral subtyping, alignment,
maximum likelihood phylogenetic tree constructed
(http://indra.mullins.microbiol.washington.edu/cgi-bin/DIVER/diver.cgi)
including unrelated sequences from each study site- Reference
datasets within infected individuals, between transmission pairs
(mother-infant, heterosexual, MSM), between epidemiologically
unlinked sequences of each subtype- Linkage assessed through
monophyly, genetic distance, Bayesian posterior probability- Data
adjudicated by 3 independent expertsResults155 transmission pairs
evaluated (Figure 1)- Linked 108 (69.7%)- Unlinked 40 (25.8%)-
Indeterminate 7 (4.5%)- Linkage by consensus env in 91 (84.3%), gag
in 9 (8.3%), SM env in 8 (7.4%)Figure 2 highlights the pairs linked
in gag for the subtype C/CRF10 tree.Figure 4 shows examples of
linked, unlinked and indeterminate pairs.Viral Subtype- Env A 43%,
C 43%, D 13% 2% intersubtype recombinants, G
