Title: Transmission clusters in the HIV-1 epidemic among men who have sex with men in Montreal, Quebec, Canada,
Abstract: Background. Several studies have used phylogenetics to investigate Human
Immunodeficiency Virus (HIV) transmission among Men who have Sex with Men
(MSMs) in Montreal, Quebec, Canada, revealing many transmission clusters. The
Quebec HIV genotyping program sequence database now includes viral sequences
from close to 4,000 HIV-positive individuals classified as MSMs. In this paper,
we investigate clustering in those data by comparing results from several
methods: the conventional Bayesian and maximum likelihood-bootstrap methods,
and two more recent algorithms, DM-PhyClus, a Bayesian algorithm that produces
a measure of uncertainty for proposed partitions, and the Gap Procedure, a fast
distance-based approach. We estimate cluster growth by focusing on recent cases
in the Primary HIV Infection (PHI) stage. Results. The analyses reveal
considerable overlap between cluster estimates obtained from conventional
methods. The Gap Procedure and DM-PhyClus rely on different cluster definitions
and as a result, suggest moderately different partitions. All estimates lead to
similar conclusions about cluster expansion: several large clusters have
experienced sizeable growth, and a few new transmission clusters are likely
emerging. Conclusions. The lack of a gold standard measure for clustering
quality makes picking a best estimate among those proposed difficult. Work
aiming to refine clustering criteria would be required to improve estimates.
Nevertheless, the results unanimously stress the role that clusters play in
promoting HIV incidence among MSMs.