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 178 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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Analysis of genotype resistance and HIV‐1 transmission risk in HIV‐1‐infected men who have sex with men in Guiyang, China

Qin,

Hong,

Wang

et al. 2024

Immunity Inflam & Disease

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BackgroundAs the social economy has developed and population mobility has increased, differences in the Human immunodeficiency virus type 1 (HIV‐1) genotype distribution among men who have sex with men (MSM) have become apparent in the provinces and cities across China. The high variability and drug resistance characteristics of HIV‐1 can lead to the widespread spread of resistant strains, which may also result in antiretroviral therapy failure and an increase in the mortality rate.ObjectiveThe genotypic drug resistance characteristics and HIV‐1 transmission risks among HIV‐1‐infected MSM in Guiyang, Guizhou Province were analyzed in the current study. The aim of the study was to provide a scientific basis for preventing the spread of HIV‐1 strains among MSM and develop intervention measures.MethodA cross‐sectional study was conducted at the Guiyang Public Health Clinical Center. A total of 181 HIV‐1‐infected MSM who not received treatment at the center between 1 January 2020 and 31 December 2022 were selected. The HIV‐1 pol region gene fragment, including the protease and reverse transcriptase regions, was amplified by nested PCR and RT‐PCR. The maximum likelihood method was used to construct a phylogenetic tree for analyzing the HIV‐1 genotypes in MSM. HIV‐1 genotypic resistance was evaluated using the Stanford University HIV drug resistance database. A molecular transmission network of HIV was constructed and the risk of HIV‐1 transmission was determined.ResultsWe successfully amplified 173 pol gene sequences from blood samples obtained from 181 patients. The main subtype was CRF07_BC (60.69% [105/173]), followed by CRF01_AE (26.59% [46/173]), CRF08_BC (4.05% [7/173]), CRF55_01B (4.62% [8/173]), B (3.47% [6/173]), and C (0.58% [1/173]). The distribution of HIV‐1 genotypes in MSM showed that there was a significant difference in the genotype composition of HIV‐1‐infected MSM according to registered residences and ages (p < .05). The CRF55_01B subtype accounted for the lowest proportion in Guiyang City and individuals >30 years of age. Multivariate logistic regression analysis of risk factors for drug resistance in HIV‐1‐infected MSM showed that the overall prevalence of pretreatment drug‐resistant species was 12.72% (22/173), and age >30 years, CRF55_01B subtype, and CD4+ T lymphocyte count >350 cells/mm3 were risk factors for drug resistance in MSM HIV‐1 strains. Among the pretreatment drug‐resistant species, non‐nucleoside reverse transcriptase inhibitors with ≥1 drug resistant‐species accounted for 9.25% (16/173), followed by protease inhibitors at 4.05% (7/173) and nucleoside reverse transcriptase inhibitors at 1.73% (3/173). Non‐nucleoside reverse transcriptase inhibitors resistant to the CRF07_BC and CRF01_AE genotypes were predominant. The CRF55_01B genotype was shown to be most likely to carry the V179E mutation. The molecular network included CRF07_BC and B genotypes. The results of multi‐factor logistic regression analysis on the factors affecting the rate of joining the network showed that individuals >30 years of age were less likely to join the network compared to those individuals <30 years of age.ConclusionThe distribution of HIV‐1 genotypes among MSM in Guiyang is diverse and complex. The main genotypes were shown to be CRF07_BC and CRF01_AE. The drug resistance mutation rate is high and pretreatment drug‐resistant species is at a moderate level of prevalence, with NNRTIs being the most common site for drug resistance mutations. The CRF07_BC subtype and patients <30 years of age were identified as the key intervention targets in Guiyang based on the molecular transmission network. Patients should routinely undergo drug resistance testing before starting antiretroviral therapy to avoid virologic treatment failure and prevent the spread of HIV‐1‐resistant strains in MSM.

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

Cited by 178 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

Analysis of genotype resistance and HIV‐1 transmission risk in HIV‐1‐infected men who have sex with men in Guiyang, China

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