The prospect of malaria elimination in the Arabian Peninsula: a population genetic approach

An insight to better understanding cross border malaria in Saudi Arabia

BACKGROUND

Border malaria is a major obstacle for the malaria elimination in Saudi Arabia. Today, the southern border of Saudi Arabia is a region where malaria cases are resurging, and malaria control is dwindling mainly due to the humanitarian crisis and the conflict in Yemen. This study analyses the current border malaria epidemiology along the southern border of Saudi Arabia from 2015 to 2018.

METHODS

All reported cases maintained by the malaria elimination centres in Aledabi and Baish, Jazan Province, Saudi Arabia, from 2015 to 2018 were analysed to examine the epidemiological changes over time. Pearson's Chi-Square test of differences was utilized to assess differences between the characteristics of imported and local causes and between border cases. A logistic regression model was used to predict imported status was related to living along side of the border area.

RESULTS

A total of 3210 malaria cases were reported in Baish and Aledabi malaria centres between 2015 and 2018, of which 170 were classified as local cases and 3040 were classified as imported cases. Reported malaria cases were mainly among males, within the imported cases 61.5% (1868/3039) were residents of the border areas.

CONCLUSIONS

Given the complexity of cross-border malaria, creating a malaria buffer zone that covers a certain margin from both sides of the border would allow for a joint force, cross-border malaria elimination programme. To initiate a malaria elimination activity and cases reported as belonging to this zone, rather than being pushed from one country to the other, would allow malaria elimination staff to work collaboratively with local borderland residents and other stakeholders to come up with innovative solutions to combat malaria and reach malaria-free borders.

Influx of diverse, drug resistant and transmissible Plasmodium falciparum into a malaria-free setting in Qatar

BACKGROUND

Successful control programs have impeded local malaria transmission in almost all Gulf Cooperation Council (GCC) countries: Qatar, Bahrain, Kuwait, Oman, the United Arab Emirates (UAE) and Saudi Arabia. Nevertheless, a prodigious influx of imported malaria via migrant workers sustains the threat of local transmission. Here we examine the origin of imported malaria in Qatar, assess genetic diversity and the prevalence of drug resistance genes in imported Plasmodium falciparum, and finally, address the potential for the reintroduction of local transmission.

METHODS

This study examined imported malaria cases reported in Qatar, between 2013 and 2016. We focused on P. falciparum infections and estimated both total parasite and gametocyte density, using qPCR and qRT-PCR, respectively. We also examined ten neutral microsatellites and four genes associated with drug resistance, Pfmrp1, Pfcrt, Pfmdr1, and Pfkelch13, to assess the genetic diversity of imported P. falciparum strains, and the potential for propagating drug resistance genotypes respectively.

RESULTS

The majority of imported malaria cases were P. vivax, while P. falciparum and mixed species infections (P. falciparum / P. vivax) were less frequent. The primary origin of P. vivax infection was the Indian subcontinent, while P. falciparum was mostly presented by African expatriates. Imported P. falciparum strains were highly diverse, carrying multiple genotypes, and infections also presented with early- and late-stage gametocytes. We observed a high prevalence of mutations implicated in drug resistance among these strains, including novel SNPs in Pfkelch13.

CONCLUSIONS

The influx of genetically diverse P. falciparum, with multiple drug resistance markers and a high capacity for gametocyte production, represents a threat for the reestablishment of drug-resistant malaria into GCC countries. This scenario highlights the impact of mass international migration on the reintroduction of malaria to areas with absent or limited local transmission.

High Plasmodium falciparum genetic diversity and temporal stability despite control efforts in high transmission settings along the international border between Zambia and the Democratic Republic of the Congo

Background

While the utility of parasite genotyping for malaria elimination has been extensively documented in low to moderate transmission settings, it has been less well-characterized in holoendemic regions. High malaria burden settings have received renewed attention acknowledging their critical role in malaria elimination. Defining the role for parasite genomics in driving these high burden settings towards elimination will enhance future control programme planning.

Methods

Amplicon deep sequencing was used to characterize parasite population genetic diversity at polymorphic Plasmodium falciparum loci, Pfama1 and Pfcsp, at two timepoints in June–July 2016 and January–March 2017 in a high transmission region along the international border between Luapula Province, Zambia and Haut-Katanga Province, the Democratic Republic of the Congo (DRC).

Results

High genetic diversity was observed across both seasons and in both countries. No evidence of population structure was observed between parasite populations on either side of the border, suggesting that this region may be one contiguous transmission zone. Despite a decline in parasite prevalence at the sampling locations in Haut-Katanga Province, no genetic signatures of a population bottleneck were detected, suggesting that larger declines in transmission may be required to reduce parasite genetic diversity. Analysing rare variants may be a suitable alternative approach for detecting epidemiologically important genetic signatures in highly diverse populations; however, the challenge is distinguishing true signals from potential artifacts introduced by small sample sizes.

Conclusions

Continuing to explore and document the utility of various parasite genotyping approaches for understanding malaria transmission in holoendemic settings will be valuable to future control and elimination programmes, empowering evidence-based selection of tools and methods to address pertinent questions, thus enabling more efficient resource allocation.

Imported and autochthonous malaria in West Saudi Arabia: results from a reference hospital

Background

The Kingdom of Saudi Arabia is seeking malaria eradication. Malaria transmission has been very low over the last few years. Discovered cases of Plasmodium falciparum infection are assigned a treatment protocol of artemisinin-based combination therapy, which consists of artesunate in addition to sulfadoxine-pyrimethamine rather than the traditional chloroquine, which has high resistance rates worldwide. This study aims to investigate the presence of different gene mutations concerning anti-malarial drug resistance (pfdhfr, pfdhps, pfmdr1, pfcrt, pfcytb, pfketch13) to identify whether drug-resistant alleles are present in this area of the Kingdom and whether the country’s treatment protocol is still suitable for Plasmodium bearing a resistance mutation.

Methods

Blood samples were collected from patients suffering from symptoms suggesting malaria coming to King Faisal Hospital, Taif, from February to August 2016. Diagnosis was performed by Giemsa-stained thin and thick blood films, rapid diagnostic test and PCR. Positive P. falciparum samples were further subjected to series of PCR amplification reactions targeting genes related with drug resistance (pfdhfr, pfdhps, pfmdr1, pfcrt, pfcytb, pfketch13).

Results

Twenty-six cases were positives, 13 infected with P. falciparum, of those, 4 cases were autochthonous, and 13 with Plasmodium vivax. The results of the gene mutation detection confirmed that there was no mutation related to resistance to artemisinin or atovaquone, on the other hand chloroquine resistance alleles were detected in 31% of samples. Moreover, point mutations in the pfdhfr and pfdhps genes, related resistance to antifolate drugs, were detected in all characterized samples.

Conclusions

Haplotypes of P. falciparum in the western region of the Kingdom of Saudi Arabia exhibit high resistance against antifolate drugs. These results should be extensively discussed when planning to modify anti-malarial drug protocols in the future.

Entomological aspects and the role of human behaviour in malaria transmission in a highland region of the Republic of Yemen

Background

The Republic of Yemen has the highest incidence of malaria in the Arabian Peninsula, yet little is known of its vectors or transmission dynamics.

Methods

A 24-month study of the vectors and related epidemiological aspects of malaria transmission was conducted in two villages in the Taiz region in 2004–2005.

Results

Cross-sectional blood film surveys recorded an overall malaria infection rate of 15.3 % (250/1638), with highest rates exceeding 30 % in one village in May and December 2005. With one exception, Plasmodium malariae, all infections were P.falciparum. Seven Anopheles species were identified among 3407 anophelines collected indoors using light traps (LT) and pyrethrum knockdown catches (PKD): Anopheles arabiensis (86.9 %), An. sergentii (9 %), An. azaniae, An. dthali, An. pretoriensis, An. coustani and An. algeriensis. Sequences for the standard barcode region of the mitochondrial COI gene confirmed the presence of two morphological forms of An. azaniae, the typical form and a previously unrecognized form not immediately identifiable as An. azaniae. ELISA detected Plasmodium sporozoites in 0.9 % of 2921 An. arabiensis (23 P. falciparum, two P. vivax) confirming this species as the primary malaria vector in Yemen. Plasmodium falciparum sporozoites were detected in An. sergentii (2/295) and a single female of An. algeriensis, incriminating both species as malaria vectors for the first time in Yemen. A vector in both wet and dry seasons, An. arabiensis was predominantly anthropophilic (human blood index = 0.86) with an entomological inoculation rate of 1.58 infective bites/person/year. Anopheles sergentii fed on cattle (67.3 %) and humans (48.3; 20.7 % mixed both species), but only 14.7 % were found in PKDs, indicating predominantly exophilic behaviour. A GIS analysis of geographic and socio-economic parameters revealed that An. arabiensis were significantly higher (P < 0.001) in houses with televisions, most likely due to the popular evening habit of viewing television collectively in houses with open doors and windows.

Conclusions

The predominantly indoor human biting vectors recorded in this study could be targeted effectively with LLINs, indoor residual spraying and/or insecticide-treated window/door curtains reinforced by education to instil a perception that effective and affordable malaria prevention is achievable.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-016-1179-8) contains supplementary material, which is available to authorized users.

Genetic Diversity of Plasmodium falciparum in Haiti: Insights from Microsatellite Markers

Hispaniola, comprising Haiti and the Dominican Republic, has been identified as a candidate for malaria elimination. However, incomplete surveillance data in Haiti hamper efforts to assess the impact of ongoing malaria control interventions. Characteristics of the genetic diversity of Plasmodium falciparum populations can be used to assess parasite transmission, which is information vital to evaluating malaria elimination efforts. Here we characterize the genetic diversity of P. falciparum samples collected from patients at seven sites in Haiti using 12 microsatellite markers previously employed in population genetic analyses of global P. falciparum populations. We measured multiplicity of infections, level of genetic diversity, degree of population geographic substructure, and linkage disequilibrium (defined as non-random association of alleles from different loci). For low transmission populations like Haiti, we expect to see few multiple infections, low levels of genetic diversity, high degree of population structure, and high linkage disequilibrium. In Haiti, we found low levels of multiple infections (12.9%), moderate to high levels of genetic diversity (mean number of alleles per locus = 4.9, heterozygosity = 0.61), low levels of population structure (highest pairwise F_st = 0.09 and no clustering in principal components analysis), and moderate linkage disequilibrium (ISA = 0.05, P<0.0001). In addition, population bottleneck analysis revealed no evidence for a reduction in the P. falciparum population size in Haiti. We conclude that the high level of genetic diversity and lack of evidence for a population bottleneck may suggest that Haiti’s P. falciparum population has been stable and discuss the implications of our results for understanding the impact of malaria control interventions. We also discuss the relevance of parasite population history and other host and vector factors when assessing transmission intensity from genetic diversity data.

Plasmodium falciparum population structure in Sudan post artemisinin-based combination therapy

Over the past decade, Sudan has stepped up malaria control backed by WHO, and this has resulted in significant reduction in parasite rate, malaria morbidity and mortality. The present study analyzed Plasmodium falciparum parasites in four geographical separated areas, to examine whether the success in malaria control following the use of artemisinin-based combination therapy (ACT) has disrupted the population structure and evolution of the parasite. We examined 319 P. falciparum isolates collected between October 2009 and October 2012 in four different areas in Sudan (Jazira [central Sudan], Southern Darfur [western Sudan], Upper Nile [southern Sudan] and Kasala [eastern Sudan]). Twelve microsatellites were analyzed for allelic diversity, multi-locus haplotype and inter-population differentiation. Level of diversity was compared to that detected for three of the above microsatellites among P. falciparum parasites in central and eastern Sudan in 1999, prior to introduction of ACT. Diversity at each locus (unbiased heterozygosity [H]) was high in all areas (Jazira, H=0.67), (Southern Darfur, H=0.71), (Upper Nile, H=0.71), and (Kasala, H=0.63). Microsatellites were distributed widely and private alleles, detected in a single population, were rare. The extent of diversity in the above sites was similar to that seen, in 1999, in central (Khartoum, H=0.73) and eastern Sudan (Gedaref, H=0.75). Significant Linkage disequilibrium (LD) was observed between the microsatellites in all populations. Pairwise FST analysis revealed that parasites in the four areas could be considered as one population. However, the parasites in Sudan clustered away from parasites in West Africa and the Arabian Peninsula. Despite marked reduction in malaria risk in Sudan, the extent of diversity and parasite genetic structure are indicative of a large population size. Further considerable reduction in transmission would be needed before fragmented sub-population can be seen. In addition, the large divergence of P. falciparum in Sudan from West Africa and Arabian Peninsula populations may result from differential evolutionary pressures acting at the population level, which shall be considered in eradication plans.

Phylogeography of var gene repertoires reveals fine-scale geospatial clustering of Plasmodium falciparum populations in a highly endemic area

Plasmodium falciparum malaria is a major global health problem that is being targeted for progressive elimination. Knowledge of local disease transmission patterns in endemic countries is critical to these elimination efforts. To investigate fine-scale patterns of malaria transmission, we have compared repertoires of rapidly evolving var genes in a highly endemic area. A total of 3680 high-quality DBLα-sequences were obtained from 68 P. falciparum isolates from ten villages spread over two distinct catchment areas on the north coast of Papua New Guinea (PNG). Modelling of the extent of var gene diversity in the two parasite populations predicts more than twice as many var gene alleles circulating within each catchment (Mugil = 906; Wosera = 1094) than previously recognized in PNG (Amele = 369). In addition, there were limited levels of var gene sharing between populations, consistent with local parasite population structure. Phylogeographic analyses demonstrate that while neutrally evolving microsatellite markers identified population structure only at the catchment level, var gene repertoires reveal further fine-scale geospatial clustering of parasite isolates. The clustering of parasite isolates by village in Mugil, but not in Wosera was consistent with the physical and cultural isolation of the human populations in the two catchments. The study highlights the microheterogeneity of P. falciparum transmission in highly endemic areas and demonstrates the potential of var genes as markers of local patterns of parasite population structure.