Structural Centrality Versus Inferred Ancestral State: Unraveling Hidden Heterogeneity in Large HIV Molecular Clusters

Large HIV molecular clusters are often treated as homogeneous units, obscuring internal heterogeneity and the distinction between contemporary transmission hubs and inferred ancestral states. Using 935 CRF55_01B pol sequences (2008–2020, Guangzhou), we constructed a Tamura-Nei 93 molecular network. The 110-member giant component (GC) was partitioned via Louvain, and bridging members were identified. Phylogenetic analysis and PastML ancestral state reconstruction were performed, with sensitivity analysis at an alternative genetic distance threshold. Louvain identified 11 communities with a core-periphery architecture. Community 1 (C1) served as the dominant structural hub, driven by 21 bridging members who accounted for 82.5% of inter-community links and exhibited significantly higher degree centrality and shorter average shortest path length than non-bridging members (p < 0.05). However, ancestral state reconstruction most frequently assigned the root state to Community 2, revealing a striking discordance between structural centrality and inferred ancestry. At the 0.008 threshold, the GC expanded substantially, yet C1 persistently remained the primary hub, preserving this decoupling. Community-level analysis unravels hidden heterogeneity and decouples structural centrality from inferred ancestral state. Bridging-member identification highlights structurally important individuals for enhanced surveillance and further evaluation.