Molecular Surveillance of malaria in Nigeria reveals expansion of chloroquine-sensitive infections.

Background The success of malaria elimination in sub-Saharan Africa rests largely on the sustained efficacies of the control and prevention chemointerventions used in malaria treatment and chemoprophylaxis in the highest-burden countries. Data on the impact of these interventions can guide policy for sustained malaria control towards elimination. We report the complexity of infection and genetic diversity of Plasmodium falciparum in Nigeria and their antimalarial resistance profiles. Methods We used targeted amplicon sequencing techniques to analyse 895 Plasmodium falciparum clinical isolates collected from the six geopolitical zones of Nigeria, mostly between 2017 and 2021. Genotypes determined from 101 single nucleotide polymorphisms (SNPs) and 36 non-synonymous amino acid mutations associated with antimalarial drug resistance were used to determine the Complexity of infection (COI), drug resistance haplotypes and genetic diversity of the parasites. Results Overall, there was a high complexity of infection, with 30.1 to 31.3% of the infections having more than a single genetically distinct parasite clone. 55.1% of the parasite isolates carried wildtype alleles of the chloroquine transporter gene, Pfcrt codons 74 to 76. The chloroquine-resistant haplotype CVIET was in 26.5% as mono-infections and 14.4% as mixed infections, with an overall presence of 40.9%. High frequencies of sulfadoxine-pyrimethamine (SP) resistance at Pfdhfr loci (50%) were observed and the Pfdhps A437G mutation was detected in 87.3% of infections. Wild-type haplotypes for Pfkelch13 were detected, although 12 non-synonymous mutations, were observed. Conclusion Sustained molecular surveillance for malaria in high-burden countries can support the implementation of current and new malaria strategies for malaria control and elimination.