Exploring HIV-1 Transmission Dynamics by Combining Phylogenetic Analysis and Infection Timing

Abstract

HIV-1 pol sequences obtained through baseline drug resistance testing of patients newly diagnosed between 2013 and 2017 were analyzed for genetic similarity. For 927 patients the information on genetic similarity was combined with demographic data and with information on the recency of infection. Overall, 48.3% of the patients were genetically linked with 11.4% belonging to a pair and 36.9% involved in a cluster of ≥3 members. The percentage of early diagnosed (≤4 months after infection) was 28.6%. Patients of Belgian origin were more frequently involved in transmission clusters (49.7% compared to 15.3%) and diagnosed earlier (37.4% compared to 12.2%) than patients of Sub-Saharan African origin. Of the infections reported to be locally acquired, 69.5% were linked (14.1% paired and 55.4% in a cluster). Equal parts of early and late diagnosed individuals (59.9% and 52.4%, respectively) were involved in clusters. The identification of a genetically linked individual for the majority of locally infected patients suggests a high rate of diagnosis in this population. Diagnosis however is often delayed for >4 months after infection increasing the opportunities for onward transmission. Prevention of local infection should focus on earlier diagnosis and protection of the still uninfected members of sexual networks with human immunodeficiency virus (HIV)-infected members.

Keywords: human immunodeficiency virus (HIV); molecular epidemiology; phylogenetic analysis; prevention; transmission dynamics; transmission networks and clusters.

Figure 1

Phylogenetic tree of sequences from human immunodeficiency virus (HIV)-1 infected patients newly diagnosed in Belgium between 2013 and 2017. Tree branches are colored according to subtype. The tree is rooted on a reference subtype J sequence.

Figure 2

Position in the phylogenetic tree (isolated, paired or clustered, %) for the complete study population (all, n = 927), the early diagnosed (n = 265), late diagnosed (n = 662), early diagnosed of Belgian origin (n = 134), late diagnosed of Belgian origin (n = 224), early diagnosed of Sub-Saharan African origin (n = 24), late diagnosed of Sub-Saharan African origin (n = 172), early diagnosed locally infected (n = 127), and late diagnosed locally infected (n = 185).