Accumulated pre-switch resistance to more recently introduced one-pill-once-a-day antiretroviral regimens impacts HIV-1 virologic outcome

Added Value of Next Generation Sequencing in Characterizing the Evolution of HIV-1 Drug Resistance in Kenyan Youth

Drug resistance remains a global challenge in children and adolescents living with HIV (CALWH). Characterizing resistance evolution, specifically using next generation sequencing (NGS) can potentially inform care, but remains understudied, particularly in antiretroviral therapy (ART)-experienced CALWH in resource-limited settings. We conducted reverse-transcriptase NGS and investigated short-and long-term resistance evolution and its predicted impact in a well-characterized cohort of Kenyan CALWH failing 1st-line ART and followed for up to ~8 years. Drug resistance mutation (DRM) evolution types were determined by NGS frequency changes over time, defined as evolving (up-trending and crossing the 20% NGS threshold), reverting (down-trending and crossing the 20% threshold) or other. Exploratory analyses assessed potential impacts of minority resistance variants on evolution. Evolution was detected in 93% of 42 participants, including 91% of 22 with short-term follow-up, 100% of 7 with long-term follow-up without regimen change, and 95% of 19 with long-term follow-up with regimen change. Evolving DRMs were identified in 60% and minority resistance variants evolved in 17%, with exploratory analysis suggesting greater rate of evolution of minority resistance variants under drug selection pressure and higher predicted drug resistance scores in the presence of minority DRMs. Despite high-level pre-existing resistance, NGS-based longitudinal follow-up of this small but unique cohort of Kenyan CALWH demonstrated continued DRM evolution, at times including low-level DRMs detected only by NGS, with predicted impact on care. NGS can inform better understanding of DRM evolution and dynamics and possibly improve care. The clinical significance of these findings should be further evaluated.

Not all clusters are equal: dynamics of molecular HIV-1 clusters in a statewide Rhode Island epidemic

OBJECTIVES

Molecular epidemiology is a powerful tool to characterize HIV epidemics and prioritize public health interventions. Typically, HIV clusters are assumed to have uniform patterns over time. We hypothesized that assessment of cluster evolution would reveal distinct cluster behavior, possibly improving molecular epidemic characterization, towards disrupting HIV transmission.

DESIGN

Retrospective cohort.

METHODS

Annual phylogenies were inferred by cumulative aggregation of all available HIV-1 pol sequences of individuals with HIV-1 in Rhode Island (RI) between 1990 and 2020, representing a statewide epidemic. Molecular clusters were detected in annual phylogenies by strict and relaxed cluster definition criteria, and the impact of annual newly-diagnosed HIV-1 cases to the structure of individual clusters was examined over time.

RESULTS

Of 2153 individuals, 31% (strict criteria) - 47% (relaxed criteria) clustered. Longitudinal tracking of individual clusters identified three cluster types: normal, semi-normal and abnormal. Normal clusters (83-87% of all identified clusters) showed predicted growing/plateauing dynamics, with approximately three-fold higher growth rates in large (15-18%) vs. small (∼5%) clusters. Semi-normal clusters (1-2% of all clusters) temporarily fluctuated in size and composition. Abnormal clusters (11-16% of all clusters) demonstrated collapses and re-arrangements over time. Borderline values of cluster-defining parameters explained dynamics of non-normal clusters.

CONCLUSIONS

Comprehensive tracing of molecular HIV clusters over time in a statewide epidemic identified distinct cluster types, likely missed in cross-sectional analyses, demonstrating that not all clusters are equal. This knowledge challenges current perceptions of consistent cluster behavior over time and could improve molecular surveillance of local HIV epidemics to better inform public health strategies.

Longitudinal typing of molecular HIV clusters in a statewide epidemic

BACKGROUND

HIV molecular epidemiology is increasingly integrated into public health prevention. We conducted cluster typing to enhance characterization of a densely sampled statewide epidemic towards informing public health.

METHODS

We identified HIV clusters, categorized them into types, and evaluated their dynamics between 2004 and 2019 in Rhode Island. We grouped sequences by diagnosis year, assessed cluster changes between paired phylogenies, t0 and t1, representing adjacent years and categorized clusters as stable (cluster in t0 phylogeny = cluster in t1 phylogeny) or unstable (cluster in t0 ≠ cluster in t1). Unstable clusters were further categorized as emerging (t1 phylogeny only) or growing (larger in t1 phylogeny). We determined proportions of each cluster type, of individuals in each cluster type, and of newly diagnosed individuals in each cluster type, and assessed trends over time.

RESULTS

A total of 1727 individuals with available HIV-1 subtype B pol sequences were diagnosed in Rhode Island by 2019. Over time, stable clusters and individuals in them dominated the epidemic, increasing over time, with reciprocally decreasing unstable clusters and individuals in them. Conversely, proportions of newly diagnosed individuals in unstable clusters significantly increased. Within unstable clusters, proportions of emerging clusters and of individuals in them declined; whereas proportions of newly diagnosed individuals in growing clusters significantly increased over time.

CONCLUSION

Distinct molecular cluster types were identified in the Rhode Island epidemic. Cluster dynamics demonstrated increasing stable and decreasing unstable clusters driven by growing, rather than emerging clusters, suggesting consistent in-state transmission networks. Cluster typing could inform public health beyond conventional approaches and direct interventions.

Outcomes of Integrase Inhibitor-based Antiretroviral Therapy in a Clinical Cohort of Treatment-experienced Children, Adolescents and Young Adults With HIV Infection

BACKGROUND

Data on integrase strand transfer inhibitor (INSTI) use in children, adolescents and young adults with HIV are limited. We evaluated virologic and safety outcomes following INSTI initiation among treatment-experienced children, adolescents and young adults.

METHODS

The DC Cohort is a multicenter observational study of individuals receiving HIV care in Washington, DC. This analysis included treatment-experienced participants 0-24 years of age who initiated an INSTI during 2011-2017. Viral suppression (VS) and safety outcomes were quantified. Differences in VS by age, sex and CD4 count were assessed using Kaplan-Meier curves.

RESULTS

Of 141 participants (median age 20 years; 35% <18 years; 60% male; 89% Black; 62% perinatally-infected), 35% had VS and 65% lacked VS on INSTI initiation. Dolutegravir was the most commonly prescribed INSTI (55%). Among participants without VS at INSTI initiation, 46% achieved VS after a median of 2.7 months. Participants 13-24 (vs. 0-12) years old (P = 0.011) and participants with CD4 counts <350 (vs. >500) cells/μL were less likely to achieve VS (P < 0.001). Among participants with VS at INSTI initiation, 51% sustained VS through a median of 11.0 months of follow-up; of the 49% with transient viremia, 77% later achieved VS again. There were no safety concerns associated with the use of INSTIs.

CONCLUSIONS

More than half of treatment-experienced children, adolescents and young adults with detectable viremia at INSTI initiation did not achieve VS, while half of those with prior VS experienced transient viremia. Further evaluation of long-term outcomes associated with INSTI use among children, adolescents and young adults is warranted.