Next-generation sequencing provides an added value in determining drug resistance and viral tropism in Cameroonian HIV-1 vertically infected children

Abstract

With limited and low-genetic barrier drugs used for the prevention of mother-to-child transmission (PMTCT) of HIV in sub-Saharan Africa, vertically transmitted HIV-1 drug-resistance (HIVDR) is concerning and might prompt optimal pediatric strategies.The aim of this study was to ascertain HIVDR and viral-tropism in majority and minority populations among Cameroonian vertically infected children.A comparative analysis among 18 HIV-infected children (7 from PMTCT-exposed mothers and 11 from mothers without PMTCT-exposure) was performed. HIVDR and HIV-1 co-receptor usage was evaluated by analyzing sequences obtained by both Sanger sequencing and ultra-deep 454-pyrosequencing (UDPS), set at 1% threshold.Overall, median (interquartile range) age, viremia, and CD4 count were 6 (4–10) years, 5.5 (4.9–6.0) log10 copies/mL, and 526 (282–645) cells/mm3, respectively. All children had wild-type viruses through both Sanger sequencing and UDPS, except for 1 PMTCT-exposed infant harboring minority K103N (8.31%), born to a mother exposed to AZT+3TC+NVP. X4-tropic viruses were found in 5 of 15 (33.3%) children (including 2 cases detected only by UDPS). Rate of X4-tropic viruses was 0% (0/6) below 5 years (also as minority species), and became relatively high above 5 years (55.6% [5/9], P = .040. X4-tropic viruses were higher with CD4 ≤15% (4/9 [44.4%]) versus CD4 >15% (1/6 [16.7%], P = .580); similarly for CD4 ≤200 (3/4 [75%]) versus CD4 >200 (2/11 [18.2%] cells/mm3, P = .077.NGS has the ability of excluding NRTI- and NNRTI-mutations as minority species in all but 1 children, thus supporting the safe use of these drug-classes in those without such mutations, henceforth sparing ritonavir-boosted protease inhibitors or integrase inhibitors for the few remaining cases. In children under five years, X4-tropic variants would be rare, suggesting vertical-transmission with CCR5-tropic viruses and possible maraviroc usage at younger ages.

HIV-1 Drug Resistance and Genetic Diversity among Vertically Infected Cameroonian Children

“…This confirms the event of early ART failure among children and the need for timeous viral load monitoring, as previously reported in the several settings of the same country [14,22,34]. This early ART failure associated with high rate of HIVDR should be addressed critically, as this may indicate a rapid selection of DRMs pre-existing as minority variants upon pharmacological pressure [34,36,37], and/or compliance challenges as children grow towards adolescence [15,39].…”

“…This high rate of PDR is far different from previous reports in the same country (4.9% around 2010) [34], and beyond the WHO's threshold for PDR [31], a disparity mainly attributed to the scale of PMTCT interventions [35]. Thus, with increasing access to option B+, PDR would be present in more than half of HIV-positive infants, especially with the use of next generation sequencing platforms [36]. Surprisingly, PDR was also high among children reported to have no exposure to ARV.…”

HIV-1 Drug Resistance and Genetic Diversity among Vertically Infected Cameroonian Children and Adolescents

“…CRF02_AG) on emerging DRMs. 29, 31 Therefore, although HIV variability may be associated to viral fitness, disease progression and drug susceptibility, 41 our findings reveal that subtype disparity might not have a major clinical relevance in the Cameroonian pediatric context at the moment. 34, 36 Our study has some limitations.…”

“…30 Thus, with increasing access to option B+, PDR would be present in more than half of HIV-positive infants, especially with the use of next generation sequencing platforms. 31 Surprisingly, PDR was also high among children reported to have no exposure to ARV. This is likely due to selection bias attributed to inadequate maternal recall of previous PMTCT interventions (which could have been resolved by measuring for drug concentration), as previously reported around 25% by Chakanyuka-Musanhu et al, in 2013.…”

Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences

“…Sequencing is increasingly utilised in the clinical management of HBV infection to inform on prognosis, treatment choice, drug resistance and to provide insight into complex cases (39,40). Whilst progress in applying new sequencing technologies to HBV has been slow to date, we are now entering an era of rapid change.…”