Integrase inhibitors (INIs) are a potent option for HIV treatment. Limited data exist on INI resistance in West Africa, particularly in children living with HIV/AIDS. We determined the prevalence of integrase gene polymorphisms and the frequency of naturally occurring amino acid (aa) substitutions at positions associated with INI resistance. Dried blood spot (DBS) samples were obtained from one hundred and seven (107) HIV-1-infected children aged less than 15 years old in two West African countries, Benin and Mali. All children were naïve to INI treatment, 56 were naïve to anti-retroviral therapy (ART), and 51 had received ART. Genetic sequencing of HIV integrase was successful in 75 samples. The aa changes at integrase positions associated with INI resistance were examined according to the Stanford HIV Genotypic Resistance database. The median ages were 2.6 and 10 years for ART-naïve and -treated children, respectively. The most common subtypes observed were CRF02_AG (74.7%) followed by CRF06_cpx (20%). No major INI-resistance mutations at positions 66, 92, 121, 143, 147, 148, 155, and 263 were detected. The most prevalent INI accessory resistance mutations were: L74I/M (14/75, 18.6%) followed by E157Q (8/75, 10.6%), G163E/N/T/Q (5/75, 6.6%), Q95A/H/P (2/75, 2.6%), and T97A (4/75, 5.3%). Other substitutions observed were M50I/L/P, H51E/P/S/Q, I72V, T112V, V201I, and T206S. Polymorphisms at positions which may influence the genetic barrier and/or drive the selection of specific INI-resistance pathways were detected. However, no transmitted drug resistance (TDR) to INI was detected among samples of INI-naïve patients. These findings support the use of this treatment class for children with HIV-1, particularly in West Africa.

Background: Exposure of Plasmodium falciparum to host immune system and antimalarials pressure leads the parasite to exploit genetic factors such as genome sequence variation (structural variation and single nucleotide polymorphism) to withstand environmental conditions. Gene copy number variation (CNVs) is a type of genome sequence polymorphism and it has been shown that CNVs contribute to parasite adaptation to environmental pressure, acquisition of drug resistance and enable the parasite to escape from host immune system. In this study, we explored CNVs in P.falciparum three putative genes related to drug pressure.Method: Blood samples were obtained from asymptomatic school children collected from December 2016 to October 2018 in Mbita sub-county, western Kenya. Genomic DNA was extracted using ISOLATE II Genomic DNA kit (Bioline, UK) following the manufacturer’s instructions. Real-time quantitative PCR was performed and the target genes copy numbers were determined by absolute quantification method.Results: The findings revealed differential level of copy number variation in target genes investigated. One isolate (KE024/18) was found to contain 5.29 copies of Pfcoronin gene, t(2) = 27.91, P = 0.0013, 95% CI [3.62 - 4.95]. In the Pfcysteine desulfurase gene, similar level of copy amplification was observed in the OS0149/18, (5.09 copies) t(2) = 7.85, P = 0.0148, 95% CI [1.85 – 6.33]. These two isolates were found to harbour the highest level of CNVs of the corresponding genes. Pfplasmepsin 2 gene was found to be less polymorphic, however, three isolates showed high copy amplification, OS062/17 (9.63 copies), t(2) = 80.50, P = 0.0002, 95% CI [8.01 – 9.09]; AL106/16 (9.18 copies), t(2) = 28.61, P = 0.0012, 95% CI [6.95 – 9.41], and KM019/18 (9.41 copies), t(2) = 90.51, P = 0.0001, 95% CI [8.01 – 8.81].Conclusion: The results show gene copy number variation in the clinical samples we explored. The findings suggest that P.falciparum may be under drug pressure in the study area, therefore, this calls for close surveillance of drug resistance.