Temporal changes in genetic diversity of msp-1, msp-2, and msp-3 in Plasmodium falciparum isolates from Grande Comore Island after introduction of ACT

Malaria is a major infectious disease that led to ~ 212 million clinical cases and about 429,000 deaths worldwide in 2016 [1]. Plasmodium falciparum malaria had been widely distributed throughout the Union of Comoros (Grande Comore, Moheli, and Anjouan Islands) and posed a serious impediment to socioeconomic development historically [2]. To effectively control malaria in Comoros, many malaria control measures have been deployed since 2000s, including indoor residual sprayings (IRS), long-lasting insecticide nets (LLINs), artemisinin-based combination therapy (ACT), intermittent presumptive treatment (IPT) for all pregnant women, and, particularly, mass drug administration (MDA) of ACT. These malaria control measures have resulted in substantial decrease malaria infection, from 108,260 cases in 2006 to 1072 in 2015 (about 99.0% decline) in Comoros, with no malaria-related deaths. However, despite the great efforts in malaria control, the annual malaria cases increased from 2015 (1072 cases) to 2016 (1372 cases) in Comoros, and the threat of future malaria outbreak remains. Furthermore, malaria transmission intensity differs among the three islands of Comoros (Grande Comore, Moheli, and Anjouan Islands). In Anjouan and Moheli, there was a limited numbers of malaria annual cases during 2014 to 2016 (7 and 5 in 2014; 3 and 8 in 2015; 4 and 6 in 2016, respectively) without local malaria infection; in contrast, the Grande Comore accounted for about 99% of the total of malaria annual cases reported in Comoros during 2013–2016 (e.g. 53,979 in 2013; 2130 in 2014; 1061 in 2015; 1362 in 2016) due to low coverage level of ACT-based MDA. To achieve an ambitious goal of completely eliminating malaria by 2020 in Comoros, there is an urgent need to develop effective and affordable malaria control and treatment strategies.

To date, several malaria pre-erythrocytic (RTS/S and PfSPZ Vaccine) or erythrocytic (MSP-1, MSP-2, and MSP-3) stage vaccines have been designed to induce immunity against the pre-erythrocytic or erythrocytic stage of the malaria parasites, respectively [3, 4]. Although several vaccines are now being tested in clinical Phase I and II trials (MSP-1, MSP-2, and MSP-3) or even have completed the pivotal Phase III clinical testing (RTS/S), the efficacies of these vaccines have been low, with limited impact against clinical malaria [5, 6]. One of the difficulties in developing an effective vaccine against P. falciparum parasite is the extensive genetic diversity of vaccine targets allowing parasites with mutated genes to escape from the host’s immune response [7, 8]. Thus, studying genetic diversity of malaria parasites in endemic areas may provide important information to improve vaccine design. Additionally, the genetic diversity of P. falciparum parasites has been widely used as an indicator of level of malaria transmission intensity in endemic regions, thus serving as a tool to evaluate the effectiveness of malaria control and intervention.

Polymorphic genetic marks, such as microsatellites and genes encoding merozoite surface proteins (msp-1, msp-2, and msp-3) have been widely used for characterization of parasite genetic diversity [9, 10]. Currently, only one study described the genetic structure of P. falciparum parasites collected from Comoros Archipelago (Grande Comore, Moheli, Anjouan, and Mayotte) using microsatellite loci [11], showing that microsatellite genotypes of the P. falciparum populations in Grande Comore were substantially different from those in other two islands (Moheli and Anjouan). Currently, no data on temporal changes in genetic diversity of P. falciparum isolates from Grande Comoros after introduction of ACT are available. Herein, the objective of this study is to investigate the dynamics of genetic diversity and multiplicity of infection (MOI) in clinical P. falciparum isolates from Grande Comore during two different periods (2006‒2007 and 2013‒2016) using polymorphic markers of msp-1, msp-2, and msp-3. The data in this study provide insights on parasite diversity and MOI after various malaria control measures.

Dramatic reduction in annual malaria cases has been achieved in Grande Comore through the use of ACT for the treatment of uncomplicated P. falciparum patients, ACT-based MDA, and other malaria control interventions. However, malaria continues to be one of most important public health problems on this island, which calls for monitoring changes in drug resistance status and parasite population dynamics. Determining P. falciparum genetic diversity and MOI from field samples is important for understanding the impacts of malaria control measures on parasite populations and for developing strategies to better control malaria infection. The present study investigates the temporal change of genetic diversity and MOI of Grande Comore P. falciparum populations based on msp-1, msp-2, and msp-3 genes that have been used to monitor parasite population widely [10, 15]. The present data showed that the frequencies of allelic diversity and MOI of msp-1, msp-2, and msp-3 significantly decreased in the 2013–2016 group when compared with those the 2006–2007 group, which may reflect a trend associated with decreasing malaria transmission intensity on this island.

Some msp-1 K1, MAD20, or RO33 haplotypes found in the present study have been reported in other regions of the world, including Brazil (AFS44739 with K1-5), Senegal (ABS84524 with K1-5, ABS84428 with K1-6, and ABS84432 with K1-11), Malawi (ADQ74224 with K1-12 and ADQ74227 with RO33-1), India (AFR61077 with K1-12 and AFR61093 with MAD20-3), Tanzania (BAM84405 with K1-12 and AAC69748 with RO33-1), Colombia (ACS26173 with MAD20-6), and Myanmar (ACB69813 with MAD20-6); whereas the other allele variants of msp-1 were new alleles identified in this study. The present data reveal RO33 being the dominant allelic type of msp-1 gene among Grande Comore P. falciparum isolates in both groups. RO33 has also been reported to the dominant allele in parasites collected from Malaysia [13], Brazil [16], and Gabon [17], whereas MAD20 allele was the most prevalent in Myanmar [18, 19], Thailand [18], Iran [20], Pakistan [21], and Colombia [22], Senegal [23, 24]. For parasites from French Guiana [25], Kenya [26], and Peru [27], K1 was the dominant msp-1 allelic type. For msp-2, the 3D7 type was the predominant among isolates in 2006–2007 group, similar to reports from several African countries, including Gambia [28], Cameroon [29], Congo [30], Ghana [31, 32], Senegal [14, 23, 24], Burkina Faso [33], Malawi [33], Uganda [33], and Tanzania [34]. The 3D7 allele was also major type in some Southeast Asian countries such as Cambodia [35], Iran [20], Malaysia [13, 36], Myanmar [19], Pakistan [21], Papua New Guinea [37], Thailand [18], as well as Thai-Myanmar borders [38]. In contrast, the FC27 was the dominant allele for parasites from Gabon [39], Cameroon [40], Nigeria [41]. Several previous reports indicate that the FC27 allele is associated with disease severity [42], and the 3D7 type may be the common genotype circulating in high disease transmission areas [32]. Here the data in this study show that over 10 years after the introduction of ACT, the prevalence of 3D7 allelic type in msp-2 gene is dramatically decreased, from 90.8 to 37.1%, whereas FC27 allelic type increased from 71.6 to 91.1%.

Previous reports show that polyclonal infection is more common in areas with high endemicity, and 50–100% of infections are polyclonal infections in mesoendemic and holoendemic areas [43‐45]. Furthermore, a significant association between the complexity of infection and polyclonal infections with the asymptomatic malaria was observed in malaria endemic area of Congo [46]. In the present study, more than 76 and 62% of the samples examined harboured polyclonal infections (two or three allelic types) of the msp-1 and msp-2 gene, respectively, in 2006–2007 group. The frequencies of polyclonal infections were reduced to about 29 and 28%, respectively, in the 2013–2016 group, which again suggests decreasing population diversity and/or transmission intensity. MOI is conventional index to measure of complexity of infection and intensity of transmission. A high MOI value is often observed in a hyperendemic region with high malaria transmission [21, 31, 47, 48]. In the present study, the MOI values decreased from 3.11 to 1.63 for msp-1 and from 2.75 to 1.35 for msp-2, respectively. The findings in this study are similar to those reported in southeastern Senegal [24] and Congo [30]. The present data suggest a progressive decrease of P. falciparum transmission on this island. In fact, according to a report from the Comoros Ministry of Health, the numbers of annual malaria cases in Grande Comore dramatically decreased from 92,480 (in 2006) with high level incidence (about 35%) to 1362 (in 2016) with low level incidence (about 0.3%). Therefore, the present data confirm that MOI can be used as a useful indicator for monitoring malaria transmission level in the endemic areas.

Sequence analysis revealed that the decline in the number of msp-1 haplotypes (32 for the 2013–2016 and 23 for the 2006–2007 group) among Grande Comore isolates. Similarly, the total number of haplotypes in msp-2 dramatically decreased from 29 in the 2006–2007 group (16 for FC27 and 13 for 3D7 allelic types) to 21 (13 for FC27 and 8 for 3D7 allelic types) in 2013–2016 group (about 28% decline). This is in agreement with previous reports in other countries with declining endemicity [49, 50]. However, studies from Senegal, Mozambique, and Iran indicated that the introduction of ACT in Congo has reduced the MOI but not the genetic diversity of msp-2 gene among P. falciparum isolates from children living in Southern districts of Brazzaville [30]. Again, haplotype analysis supports reduced genetic diversity and transmission on the Grande Comore island.

The polymorphism of pfmsp-3 is predominantly confined to sequence diversity in the N-terminal domain within the heptad-repeats (insertion/deletion and nucleotide substitutions) [10]. The present study detected both msp-3 K1 and 3D7, but not recombinant type, similar to those reported from Thailand, Papua New Guinea, India, Keyan [10]. Recombinant msp-3 alleles were detected in Iran and African countries at a very low frequency [51, 52]. Some of the Grande Comore parasites collected in this study had new msp-3 alleles (K1-3 to K1-8, 3D7-2 and 3D7-3) that have not been reported previously. However, many parasites showed 100% identity with those from Asia, Africa, and South America reported previously, such as Thailand (AOT86948 with K1-1, AOT86951 with K1-2, and AOT86944 with 3D7-1), India (AEI28718 with K1-1, AEI28725 with K1-2, and AEI28765 with 3D7-1), Kenya (AMM75906 with K1-1, AMM75893 with K1-2, and AMM75927 with 3D7-1), Nigeria (CAJ44166 with K1-1, CAJ44194 with K1-2, and CAJ44184 with 3D7-1), China (AAF04099 with K1-1), Indonesia (AAF59914 with K1-2), Papua New Guinea (AAC47670 with K1-2, and AAC47662 with 3D7-1), Vietnam (AAK94780 with K1-2), and Brazil (AFP75269 with K1-2). In the present study, the msp-3 3D7-1 haplotype was the most prevalent in both 2006–2007 and 2013–2016 groups. The present data were in line with the findings from Thailand, India, and Nigeria, where 3D7-1 haplotypes was the most abundant types [10]. In the present study, K1 allelic type was the predominant (66.7%) in 2006–2007 group. The data in the present study are in some degree consistent with the reports of K1 being the most prevalent type in the Thailand [10], Thailand–Myanmar border [53], and Thailand–Cambodia border [53], but is contrast to previous reports from in Thailand–Laos border [53] and Peru [54], with the 3D7 being the most prevalent type. Over the course of 10 years (from 2006 to 2016), the frequencies of K1 type dramatically decreased from 66.7 to 46.5% (P < 0.01), while the 3D7 type dramatically increased from 33.3 to 53.5% (P < 0.01), suggesting that parasites with the msp-3 3D7 type may survive better after introduction of ACTs in Grande Comore. The total number of haplotypes in msp-3 gene changed from 11 in 2006–2007 to 3 in 2013–2016 (a 60% decline), suggesting a decreasing tend in genetic diversity of msp-3 in Grande Comore after 10 years of use of ACT.

The observation of increased frequencies of msp-2 FC27 and msp-3 3D7 allelic types when general population genetic diversity and other allelic types have decreased are interesting, although we do not know the reason for the shift of the alleles. One remote possibility is that the msp-2 FC27 and/or msp-3 3D7 alleles or some unknown genes nearby (linked to msp-2 and/or msp-3) play a role in parasite response to ACT. Parasites carrying these specific alleles/genes can survive better under drug pressure and increase frequency. Another possibility is that the 2013–2016 parasite populations might consist of some parasites carrying these alleles imported from nearby endemic regions after reduction in the original parasite populations. These issues require further investigations.

This study investigated the temporal change in genetic diversity and MOI of P. falciparum populations in Grande Comore Island after the introduction of ACT using the polymorphic genetic markers (MSP-1, MSP-2, and MSP-3). Results from the current study showed that the prevalence of genetic diversity and MOI in msp-1, msp-2, or msp-3 decreased over the course of the study (July 2006 to July 2016). The data in this study suggest a progressive decrease in genetic diversity likely due to lower malaria transmission intensity. The data presented here provide a valuable information for assessing the appropriateness of the current malarial control strategies in this endemic area.