Polymorphisms in Pfcrt and Pfmdr-1 genes after five years withdrawal of chloroquine for the treatment of Plasmodium falciparum malaria in West Bengal, India

Genetic diversity and evolution pattern of Plasmodium falciparum multidrug resistance 1 gene (Pfmdr1) in Indian and global populations

BACKGROUND

Among the crucial molecular markers contributing to multidrug resistance, the Plasmodium falciparum multidrug resistance-1 gene (Pfmdr1) remains understudied as compared to other drug-resistant genes in terms of its genetic diversity and evolution pattern. This study presents a comprehensive analysis of Pfmdr1 gene's genetic diversity aiming to discern its dynamics, distribution and evolutionary trends especially in Indian and global populations.

METHODS AND RESULTS

The Pfmdr1 gene was amplified and sequenced from 256 Plasmodium falciparum mono-infected samples collected from 14 Indian states during the years 1993-2023. Analysis revealed six non-synonymous (N86Y, N86F, S137C, D144F, F157L and Y184F) and one synonymous mutation (G182G) in N-terminal fragment. Among these, N86F, S137C, D144F and F157L were novel findings. The most prevalent mutations were N86Y (18.91%), Y184F (64.71%) and G182G (GGT > GGG) (59.24%; exclusive to India), with Y184F showing increasing trend when compared to N86Y over time. The mutation GGT > GGG is experiencing a hitchhiking by Y184F mutation which is likely undergoing a selective sweep. High haplotype and nucleotide diversity were observed in most Indian states, particularly in Odisha and Delhi. However, a decrease in diversity was noted in samples from 2020 onwards throughout India. Globally Pfmdr1 showed tendency of negative selection, except for populations from Liberia, Nigeria, Sudan and Central African Republic. Notably, samples from Sudan depicted a distinct haplotype and population structure compared to other countries.

CONCLUSIONS

These findings contribute significantly to our understanding of the genetic structure and evolutionary trends of Pfmdr1, which can help to strengthen the current malaria control policies for emergence of drug resistance.

Characterization of drug resistance genes in Indian Plasmodium falciparum and Plasmodium vivax field isolates

One of the major challenges for malaria control and elimination is the spread and emergence of antimalarial drug resistance. Mutations in Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) field isolates for five drug resistance genes viz. crt, mdr1, dhps, dhfr and kelch known to confer resistance to choloroquine (CQ), sulfadoxine-pyrimethamine (SP) and artemisinin (ART) and its derivatives were analyzed. A total of 342 symptomatic isolates of P. falciparum (Pf) and P. vivax (Pv) from 1993 to 2014 were retrieved from malaria parasite repository at National Institute of Malaria Research (NIMR). Sample DNA was extracted from dried blood spots and various targeted single nucleotide polymorphisms (SNPs) associated with antimalarial drug resistance were analysed for these isolates. 72S (67.7%) and 76T (83.8%) mutations along with SVMNT haplotype (67.7%) predominated the study population for Pfcrt. The most prevalent SNPs were 108N (73.2%) and 437G (24.8%) and the most prevalent haplotypes were ACNRNI (51.9%) and SAKAA (74.5%) in Pfdhfr and Pfdhps respectively. Only two mutations in Pfmdr1, 86Y (26.31%) and 184F (56.26%), were seen frequently in our study population. No mutations associated with Pfk13 were observed. For Pv, all the studied isolates showed two Pvdhps mutations, 383G and 553G, and two Pfdhfr mutations, 58R and 117N. Similarly, three mutations, viz. 958M, 908L and 1076L were found in Pvmdr1. No variations were observed in Pvcrt-o and Pvk12 genes. Overall, our study demonstrates an increase in mutations associated with SP resistance in both Pf and Pv, however, no single nucleotide polymorphisms (SNPs) associated with ART resistance have been observed for either species. Various SNPs associated with CQ resistance were seen in Pf; whereas only Pvmdr1 associated resistant SNPs were observed in Pv. Therefore, molecular characterization of drug resistance genes is essential for timely monitoring and prevention of malaria by identifying the circulating drug resistant parasites in the country.

Prevalence of polymorphisms in marker genes associated with antimalarial drug resistance in Plasmodium falciparum following 10 years of artemisinin-based combination therapy implementation in urban Kolkata

Context

Resistance to antimalarial drugs is one of the major challenges for malaria elimination. In India, artemisinin combination therapy (artesunate-sulfadoxin pyrimethamine) was introduced in place of chloroquine (CQ) for the treatment of uncomplicated falciparum malaria in 2010. Periodical monitoring of polymorphisms in antimalarial drug resistance marker genes will be useful for assessing drug pressure, mapping and monitoring of drug resistance status; and will be helpful for searching alternative treatments.

Objectives

This study was conducted to study the polymorphisms in antimalarial drug resistance marker genes among clinical Plasmodium falciparum isolates collected from Kolkata after 10 years of artemisinin-based combination therapie (ACT) implementation.

Materials and Methods

Blood samples were collected from P. falciparum mono-infected patients and polymorphisms in P. falciparum CQ resistance transporter (pfcrt), P. falciparum multidrug resistance (pfmdr-1), P. falciparum dihydrofolate reductase (pfdhfr), P. falciparum dihydropteroate synthetase (pfdhps), pfATPase6 and pfK-13 propeller genes were analysed by polymerase chain reaction and DNA sequencing.

Results

In pfcrt gene, C72S, and K76T mutation was recorded in 100% isolates and no mutations was detected in any of the targeted codons of pfmdr-1 gene. A double mutant pfcrt haplotype SVMNT and wildtype haplotype NYD in pfmdr-1 were prevalent in 100% of study isolates. Triple mutant pfdhfr-pfdhps haplotype ANRNI-SGKAA was recorded. No polymorphism in pfK13 gene was documented in any of the isolates.

Conclusions

Observed wild codon N86 along with Y184 and D1246 of pfmdr-1 gene might be an indication of the reappearance of CQ sensitivity. The absence of quadruple and quintuple haplotypes in pfdhfr-pfdhps gene along with the wild haplotype of pfK13 is evidence of ACT effectivity. Hence, similar studies with large sample size are highly suggested for monitoring the drug resistance status of P. falciparum.

Nationwide spatiotemporal drug resistance genetic profiling from over three decades in Indian Plasmodium falciparum and Plasmodium vivax isolates

BACKGROUND

Drug resistance is a serious impediment to efficient control and elimination of malaria in endemic areas.

METHODS

This study aimed at analysing the genetic profile of molecular drug resistance in Plasmodium falciparum and Plasmodium vivax parasites from India over a ~ 30-year period (1993-2019). Blood samples of P. falciparum and/or P. vivax-infected patients were collected from 14 regions across India. Plasmodial genome was extracted and used for PCR amplification and sequencing of drug resistance genes in P. falciparum (crt, dhps, dhfr, mdr1, k13) and P. vivax (crt-o, dhps, dhfr, mdr1, k12) field isolates.

RESULTS

The double mutant pfcrt SVMNT was highly predominant across the country over three decades, with restricted presence of triple mutant CVIET from Maharashtra in 2012. High rates of pfdhfr-pfdhps quadruple mutants were observed with marginal presence of "fully resistant" quintuple mutant ACIRNI-ISGEAA. Also, resistant pfdhfr and pfdhps haplotype has significantly increased in Delhi between 1994 and 2010. For pfmdr1, only 86Y and 184F mutations were present while no pfk13 mutations associated with artemisinin resistance were observed. Regarding P. vivax isolates, the pvcrt-o K10 "AAG" insertion was absent in all samples collected from Delhi in 2017. Pvdhps double mutant SGNAV was found only in Goa samples of year 2008 for the first time. The pvmdr1 908L, 958M and 1076L mutations were highly prevalent in Delhi and Haryana between 2015 and 2019 at complete fixation. One nonsynonymous novel pvk12 polymorphism was identified (K264R) in Goa.

CONCLUSIONS

These findings support continuous surveillance and characterization of P. falciparum and P. vivax populations as proxy for effectiveness of anti-malarial drugs in India, especially for independent emergence of artemisinin drug resistance as recently seen in Africa.

Chloroquine and hydroxychloroquine in the treatment of malaria and repurposing in treating COVID-19

Chloroquine (CQ) and Hydroxychloroquine (HCQ) have been commonly used for the treatment and prevention of malaria, and the treatment of autoimmune diseases for several decades. As their new mechanisms of actions are identified in recent years, CQ and HCQ have wider therapeutic applications, one of which is to treat viral infectious diseases. Since the pandemic of the coronavirus disease 2019 (COVID-19), CQ and HCQ have been subjected to a number of in vitro and in vivo tests, and their therapeutic prospects for COVID-19 have been proposed. In this article, the applications and mechanisms of action of CQ and HCQ in their conventional fields of anti-malaria and anti-rheumatism, as well as their repurposing prospects in anti-virus are reviewed. The current trials and future potential of CQ and HCQ in combating COVID-19 are discussed.

Malaria epidemics in India: Role of climatic condition and control measures

Malaria is a major public health problem in India, which is the second most populous country in the world. This study aimed to investigate the impact of climatic parameters and malaria control efforts implemented by the Indian national malaria control program on malaria epidemics between January of 2009 and December of 2015. A chi-squared test was used to study the correlation of all implemented control methods with occurrence of epidemics within 30, 45, 60 and 90 days and in the same district, 50, 100 and 200 km distance radiuses. The effect of each control method on probability of epidemics was also measured, and the effects of district population, season, and incidence of malaria parasite types were evaluated using logistic regression models. Fever survey was found to be effective for decreasing the odds of epidemics within 45, 60 and 90 days in 100 km. Anti-larval activity was also effective within 30, 45 and 60 days in 200 km. Winter had negative effects on odds ratio while summer and fall were more likely to trigger epidemics. These results contribute to understanding the role of climate variability and control efforts performed in India.

Prevalence of mutations linked to antimalarial resistance in Plasmodium falciparum from Chhattisgarh, Central India: A malaria elimination point of view

Antimalarial drug resistance is a major global challenge in malaria control and elimination. Mutations in six different genes of Plasmodium falciparum (crt, mdr1, dhfr, dhps, ATPase6 and K-13 propeller) that confer resistance to chloroquine, sulphadoxine-pyrimethamine and artemisinin-based combination therapy were analyzed in samples from Chhattisgarh. Seventy-eight percent of the samples were found to have a pfcrt mutation (53% double, 24% triple and 1% single mutant), and 59% of pfmdr1 genes were found to have an N86Y mutation. Double mutations were recorded in pfdhfr gene among 76% of the samples while only 6% of the samples harbored mutant genotypes in pfdhps. No mutation was found in the K-13 propeller gene, while only one sample showed a mutant genotype for the PfATPase6 gene. The Tajima test confirmed that there is no role of evolutionary natural selection in drug resistance, and gene pairwise linkage of disequilibrium showed significant intragenic association. The high level of pfcrt mutations suggests that parasite resistance to chloroquine is almost at a fixed level, whereas resistance to SP is evolving in the population and parasites remain sensitive to artemisinin derivatives. These findings provide potential information and understanding of the evolution and spread of different drug resistance alleles in Chhattisgarh.

Molecular surveillance of chloroquine drug resistance markers (Pfcrt and Pfmdr1) among imported Plasmodium falciparum malaria in Qatar

Imported malaria has been a great challenge for public health in Qatar due to influx of large number of migrant workers. Antimalarial drug resistance has emerged as one of the greatest challenges facing malaria control today. Monitoring parasite haplotypes that predict susceptibility to major antimalarial can guide treatment policies. This study aimed to determine molecular drug resistance pattern in imported malaria cases in Qatar. Blood samples from the uncomplicated P. falciparum malaria patients were collected at Hamad General Hospital, HMC, Doha, Qatar. The samples were further confirmed by nested-polymerase chain reaction (PCR) for P. falciparum. Molecular markers of chloroquine (Pfcrt and Pfmdr1) were analyzed by using nested PCR- RFLP method to determine the key point mutations associated with chloroquine (CQ) drug resistance. A total 118 blood samples were positive for P. falciparum. Overall, by RFLP, 72% harboured wild type allele (N86) of Pfmdr1 gene. The prevalence of Pfcrt mutant (T76), WT (K76) and mixed alleles (K76T) was 63.6% (n = 75), 22.9% (n = 27) and 13.5% (n = 16), respectively. Mean parasitaemia level was higher among the wild type alleles of Pfcrt gene as compared to the mixed/mutant alleles whereas mixed alleles of Pfmdr1 gene having high parasitaemia. Molecular surveillance strategy based on imported malaria cases can be used to detect and track CQ drug-resistant malaria. The data presented here might be helpful for enrichment of molecular surveillance of antimalarial resistance and will be useful for developing and updating antimalarial guidance for non-immune imported cases in Qatar.

Molecular analysis demonstrates high prevalence of chloroquine resistance but no evidence of artemisinin resistance in Plasmodium falciparum in the Chittagong Hill Tracts of Bangladesh

BACKGROUND

Artemisinin resistance is present in the Greater Mekong region and poses a significant threat for current anti-malarial treatment guidelines in Bangladesh. The aim of this molecular study was to assess the current status of drug resistance in the Chittagong Hill Tracts of Bangladesh near the Myanmar border.

METHODS

Samples were obtained from patients enrolled into a Clinical Trial (NCT02389374) conducted in Alikadam, Bandarban between August 2014 and January 2015. Plasmodium falciparum infections were confirmed by PCR and all P. falciparum positive isolates genotyped for the pfcrt K76T and pfmdr1 N86Y markers. The propeller region of the kelch 13 (k13) gene was sequenced from isolates from patients with delayed parasite clearance.

RESULTS

In total, 130 P. falciparum isolates were available for analysis. The pfcrt mutation K76T, associated with chloroquine resistance was found in 81.5% (106/130) of cases and the pfmdr1 mutation N86Y in 13.9% (18/130) cases. No single nucleotide polymorphisms were observed in the k13 propeller region.

CONCLUSION

This study provides molecular evidence for the ongoing presence of chloroquine resistant P. falciparum in Bangladesh, but no evidence of mutations in the k13 propeller domain associated with artemisinin resistance. Monitoring for artemisinin susceptibility in Bangladesh is needed to ensure early detection and containment emerging anti-malarial resistance.