Social and Genetic Networks of HIV-1 Transmission in New York City

Wertheim, Joel O.; Pond, Sergei L. Kosakovsky; Forgione, Lisa A.; Mehta, Sanjay R.; Murrell, Ben; Shah, Sharmila; Smith, Davey M.; Scheffler, Konrad; Torian, Lucia V.

doi:10.1371/journal.ppat.1006000

Cited by 170 publications

(183 citation statements)

References 49 publications

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“…Owing to incomplete sampling or significant modularity of contact networks, transmission networks identified among persons at high-risk of infection are frequently organized into several components and unlinked nodes (Wertheim et al, 2017; Wertheim et al, 2014), similar to the ITN used in this study (Fig. 2).…”

Section: Discussionmentioning

confidence: 98%

“…HCV spread among high-risk populations such as PWID and men-who-have-sex-with-men (MSM) is facilitated by tight contact networks (Rolls et al, 2013), which can be modeled as transmission networks identified using genetic approaches (Wertheim et al, 2017). However, transmission networks are not frequently available to guide PHI, prompting the use of other approaches like an acquaintance network (Chami et al, 2017; Hellard et al, 2014) to estimate indirectly the underlying contact network structure.…”

Section: Discussionmentioning

confidence: 99%

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Intelligent Network DisRuption Analysis (INDRA): A targeted strategy for efficient interruption of hepatitis C transmissions

Campo

Khudyakov

2018

Infection, Genetics and Evolution

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Hepatitis C virus (HCV) infection is a global public health problem. The implementation of public health interventions (PHI) to control HCV infection could effectively interrupt HCV transmission. PHI targeting high-risk populations, e.g., people who inject drugs (PWID), are the most efficient but there is a lack of tools for prioritizing individuals within a high-risk community. Here, we present Intelligent Network DisRuption Analysis (INDRA), a targeted strategy for efficient interruption of hepatitis C transmissions. Using a large HCV transmission network among PWID in Indiana as an example, we compare effectiveness of random and targeted strategies in reducing the rate of HCV transmission in two settings: (1) long-established and (2) rapidly spreading infections (outbreak). Identification of high centrality for the network nodes co-infected with HIV or >1 HCV subtype indicates that the network structure properly represents the underlying contacts among PWID relevant to the transmission of these infections. Changes in the network’s global efficiency (GE) were used as a measure of the PHI effects. In setting 1, simulation experiments showed that a 50% GE reduction can be achieved by removing 11.2 times less nodes using targeted vs random strategies. A greater effect of targeted strategies on GE was consistently observed when networks were simulated: (1) with a varying degree of errors in node sampling and link assignment, and (2) at different levels of transmission reduction at affected nodes. In simulations considering a 10% removal of infected nodes, targeted strategies were ~2.8 times more effective than random in reducing incidence. Peer-education intervention (PEI) was modeled as a probabilistic distribution of actionable knowledge of safe injection practices from the affected node to adjacent nodes in the network. Addition of PEI to the models resulted in a 2–3 times greater reduction in incidence than from direct PHI alone. In setting 2, however, random direct PHI were ~3.2 times more effective in reducing incidence at the simulated conditions. Nevertheless, addition of PEI resulted in a ~1.7-fold greater efficiency of targeted PHI. In conclusion, targeted PHI facilitated by INDRA outperforms random strategies in decreasing circulation of long-established infections. Network-based PEI may amplify effects of PHI on incidence reduction in both settings.

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Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Intelligent Network DisRuption Analysis (INDRA): A targeted strategy for efficient interruption of hepatitis C transmissions

Campo

Khudyakov

2018

Infection, Genetics and Evolution

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“…All pairwise distances were computed and a putative linkage between two individuals was considered whenever their pol sequences were ≤0.015 substitutions/site divergent (TN93 substitution model) (31–33). When calculating pairwise genetic distance, all nucleotide ambiguities were resolved and only sequences with less than 1.5% ambiguities were retained (34). Problematic sequences, including those closely related to HXB2 and NL4-3, which could be deemed as possible contaminants, were flagged and repeated based on phylogenetic analyses performed on a monthly basis as an internal laboratory control.…”

Section: Methodsmentioning

confidence: 99%

“…Clusters comprised of only two linked nodes were identified as dyads. This approach will detect clusters of recent transmission in which the clustering viruses are genetically similar, implying a direct or indirect epidemiological connection (34). …”

Section: Methodsmentioning

confidence: 99%

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Identification of major routes of HIV transmission throughout Mesoamerica

Chaillon

Ávila‐Ríos²,

Wertheim

et al. 2017

Infection, Genetics and Evolution

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Background Migration and travel are major drivers of the spread of infectious diseases. Geographic proximity and a common language facilitate travel and migration in Mesoamerica, which in turn could affect the spread of HIV in the region. Methods 6,092 HIV-1 subtype B partial pol sequences sampled from unique antiretroviral treatment-naive individuals from Mexico (40.7%), Guatemala (24.4%), Honduras (19%), Panama (8.2%), Nicaragua (5.5%), Belize (1.4%), and El Salvador (0.7%) between 2011–2016 were included. Phylogenetic and genetic network analyses were performed to infer putative relationships between HIV sequences. The demographic and geographic associations with clustering were analyzed and viral migration patterns were inferred using the Slatkin-Maddison approach on 100 iterations of random subsets of equal number of sequences per location. Results A total of 1,685/6,088 (27.7%) of sequences linked with at least one other sequence, forming 603 putative transmission clusters (range: 2–89 individuals). Clustering individuals were significantly more likely to be younger (median age 29 vs 33 years, p<0.01) and men-who-have-sex-with-men (40.4% vs 30.3%, p<0.01). Of the 603 clusters, 30 (5%) included sequences from multiple countries with commonly observed linkages between Mexican and Honduran sequences. Eight of the 603 clusters included more than 10 individuals, including two comprised exclusively of Guatemalans (52 and 89 individuals). Phylogenetic and migration analyses suggested that the Central and Southern regions of Mexico along with Belize were major sources of HIV throughout the region (p<0.01) with genetic flow southward from Mexico to the other nations of Mesoamerica. We also found evidence of significant viral migration within Mexico. Conclusion International clusters were infrequent, suggesting moderate migration between HIV epidemics of the different Mesoamerican countries. Nevertheless, we observed important sources of transnational HIV spread in the region, including Southern and Central Mexico and Belize.

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Characteristics and growth of the genetic HIV transmission network of Mexico City during 2020

Dávila-Conn¹,

García-Morales²,

Matías-Florentino³

et al. 2021

J Int AIDS Soc.

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IntroductionMolecular surveillance systems could provide public health benefits to focus strategies to improve the HIV care continuum. Here, we infer the HIV genetic network of Mexico City in 2020, and identify actively growing clusters that could represent relevant targets for intervention.MethodsAll new diagnoses, referrals from other institutions, as well as persons returning to care, enrolling at the largest HIV clinic in Mexico City were invited to participate in the study. The network was inferred from HIV pol sequences, using pairwise genetic distance methods, with a locally hosted, secure version of the HIV‐TRACE tool: Seguro HIV‐TRACE. Socio‐demographic, clinical and behavioural metadata were overlaid across the network to design focused prevention interventions.ResultsA total of 3168 HIV sequences from unique individuals were included. One thousand and one‐hundred and fifty (36%) sequences formed 1361 links within 386 transmission clusters in the network. Cluster size varied from 2 to 14 (63% were dyads). After adjustment for covariates, lower age (adjusted odds ratio [aOR]: 0.37, p<0.001; >34 vs. <24 years), being a man who has sex with men (MSM) (aOR: 2.47, p = 0.004; MSM vs. cisgender women), having higher viral load (aOR: 1.28, p<0.001) and higher CD4+ T cell count (aOR: 1.80, p<0.001; ≥500 vs. <200 cells/mm3) remained associated with higher odds of clustering. Compared to MSM, cisgender women and heterosexual men had significantly lower education (none or any elementary: 59.1% and 54.2% vs. 16.6%, p<0.001) and socio‐economic status (low income: 36.4% and 29.0% vs. 18.6%, p = 0.03) than MSM. We identified 10 (2.6%) clusters with constant growth, for prioritized intervention, that included intersecting sexual risk groups, highly connected nodes and bridge nodes between possible sub‐clusters with high growth potential.ConclusionsHIV transmission in Mexico City is strongly driven by young MSM with higher education level and recent infection. Nevertheless, leveraging network inference, we identified actively growing clusters that could be prioritized for focused intervention with demographic and risk characteristics that do not necessarily reflect the ones observed in the overall clustering population. Further studies evaluating different models to predict growing clusters are warranted. Focused interventions will have to consider structural and risk disparities between the MSM and the heterosexual populations.

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Social and Genetic Networks of HIV-1 Transmission in New York City

Cited by 170 publications

References 49 publications

Intelligent Network DisRuption Analysis (INDRA): A targeted strategy for efficient interruption of hepatitis C transmissions

Intelligent Network DisRuption Analysis (INDRA): A targeted strategy for efficient interruption of hepatitis C transmissions

Identification of major routes of HIV transmission throughout Mesoamerica

Characteristics and growth of the genetic HIV transmission network of Mexico City during 2020

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