Targeted and whole-genome sequencing reveal a north-south divide in P. falciparum drug resistance markers and genetic structure in Mozambique

Mozambique is one of the four African countries which account for over half of all malaria deaths worldwide, yet little is known about the parasite genetic structure in that country. We performed P. falciparum amplicon and whole genome sequencing on 2251 malaria-infected blood samples collected in 2015 and 2018 in seven provinces of Mozambique to genotype antimalarial resistance markers and interrogate parasite population structure using genome-wide microhaplotyes. Here we show that the only resistance-associated markers observed at frequencies above 5% were pfmdr1-184F (59%), pfdhfr-51I/59 R/108 N (99%) and pfdhps-437G/540E (89%). The frequency of pfdhfr/pfdhps quintuple mutants associated with sulfadoxine-pyrimethamine resistance increased from 80% in 2015 to 89% in 2018 (p < 0.001), with a lower expected heterozygosity and higher relatedness of microhaplotypes surrounding pfdhps mutants than wild-type parasites suggestive of recent selection. pfdhfr/pfdhps quintuple mutants also increased from 72% in the north to 95% in the south (2018; p < 0.001). This resistance gradient was accompanied by a concentration of mutations at pfdhps-436 (17%) in the north, a south-to-north increase in the genetic complexity of P. falciparum infections (p = 0.001) and a microhaplotype signature of regional differentiation. The parasite population structure identified here offers insights to guide antimalarial interventions and epidemiological surveys.

Evaluation of a universal coverage bed net distribution campaign in four districts in Sofala Province, Mozambique

Malaria is the leading cause of death in Mozambique in children under five years old. In 2009, Mozambique developed a novel bed net distribution model to increase coverage, based on assumptions about sleeping patterns. The coverage and impact of a bed net distribution campaign using this model in four districts in Sofala Province, Mozambique was evaluated. Methods: Paired household, cross-sectional surveys were conducted one month after the 2010 distribution of 140,000 bed nets and again 14 months after the campaign in 2011. During household visits, malaria blood smears were performed and haemoglobin levels were assessed on children under five and data on bed net ownership, access and use were collected; these indicators were analysed at individual, household and community levels. Logistic regression was used to evaluate predictors of malaria infection and anaemia. Results: The campaign reached 98% (95% CI: 97-99%) of households registered during the precampaign listing, with 81% (95% CI: 77-85%) of sleeping spaces covered by campaign bed nets and 85% (95% CI: 81-88%) of the population sleeping in a sleeping space with a campaign bed net designated for the sleeping space. One year after the campaign, 65% (95% CI: 57-72%) of sleeping spaces were observed to have hanging bed nets. The proportion of sleeping spaces for which bed nets were reported used four or more times per week was 65% (95% CI: 56-74%) in the wet season and 60% (95% CI: 52-68%) in the dry season. Malaria parasitaemia prevalence in children under five years old was 47% (95% CI: 40-54%) in 2010 and 36% (95% CI: 27-45%) in 2011. Individual-level malaria infection and anaemia were significantly associated with community-level use of bed nets. Conclusions: The campaign using the novel distribution model achieved high coverage, although usage was not uniformly high. A significant decrease in malaria parasitaemia prevalence a year after the campaign was not observed, but community-level use of bed nets was significantly associated with a reduced risk for malaria infection and anaemia in children under five.