Single Genome Analysis for the Detection of Linked Multiclass Drug Resistance Mutations in HIV-1-Infected Children After Failure of Protease Inhibitor-Based First-Line Therapy

Abstract

The WHO recommends protease inhibitor (PI)–based antiretroviral therapy (ART) for vertically infected children after failed nevirapine (NVP) prophylaxis. Emergence of PI resistance on the backdrop of preexisting non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance could compromise long-term treatment options in such children. We characterized multiclass drug resistance using single genome sequencing (SGS) in children with viremia while receiving PI-based ART. We applied SGS of HIV-1 protease (PR) and reverse transcriptase to longitudinal samples from a cohort of the Children with HIV Early Antiretroviral Therapy trial with viral loads >1000 copies per milliliter after 40 weeks of early ART. Bulk sequencing revealed NVP-selected resistance in 50% of these children, whereas SGS revealed NVP-selected resistance in 70%. Two children had baseline NRTI and PI mutations, suggesting previous maternal ART. Linked multiclass drug resistance after PI-based ART was detected by SGS in 2 of 10 children. In one child, the majority species contained M184V in reverse transcriptase linked to L10F, M46I/L, I54V, and V82A in PR and a triple-class drug-resistant variant with these mutations linked to the NNRTI mutation V108I. In the second child, the majority species contained M184V and V82A linked within viral genomes. We conclude that when PI-based ART is initiated soon after birth after single dose-NVP prophylaxis, PI and NRTI resistance can occur in the majority species as expected and also be selected on the same genomes as preexisting NNRTI-resistant mutations. These observations highlight a future therapeutic challenge for vertically infected children where antiretroviral drug classes are limited.

Prevalence and effect of pre-treatment drug resistance on the virological response to antiretroviral treatment initiated in HIV-infected children – a EuroCoord-CHAIN-EPPICC joint project

“…Nevertheless pre-existing NNRTI resistance may still compromise response to PI-based first line cART. Indeed PI resistance can emerge in children with PDR as evidenced by the presence of multidrug resistance mutations in single HIV genome in children failing PI-based first line [55]. …”

Antiretroviral Treatment and Resistance Patterns in HIV-Infected Children

“…Baseline NRTI and PI mutations were detected in two of the children, suggestive of previous maternal ART use. Linked multi-class drug resistance following use of PI-based ART was detected in two of the children [25]. A South African study reported the results of resistance testing among 152 children who developed virologic failure while on first-line LPV/r-based therapy.…”

“…Lange et al [25] characterised multi-class drug resistance using single genome sequencing (SGS) of HIV-1 protease and Table 4 Major protease inhibitor resistance mutations 30 32 33 46 47 48 50 54 76 82 84 88 90 Consensus D V L M I G I I L V I …”

“…Development of PI resistance in the same patient with established NNRTI resistance limits the choices that are available for the inevitable long-term treatment options in HIV-infected children [25]. The Children with HIV Early Antiretroviral (CHER) study looked at children who had viraemia while on PI-based regimens and were characterised as having multi-class drug resistance by the use of single genome sequencing [25].…”

“…This is also consistent with the evidence that knowledge of patient's virus resistance profile prior to treatment will go a long way to avoid unnecessary stopping of a particular regimen and switching to others regimens. The cohorts showed resistance across the main ARV classes although in varying degrees [15,18,22,[24][25][26][27][28][29][30][31].…”