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Kale S, Uplekar SM, Bandyopadhyay N, Rao PN, Ali SZ, Sharma S, Tandel N, Patel A, Singh R, Dank A, Ravishankaran S, Lakshmi Priya GS, Asokan A, Eapen A, Singh OP, Carlton JM, Mallick PK. Antimalarial Drug Resistance Profiling of Plasmodium falciparum Infections in India Using Next-Generation Sequencing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.08.23288321. [PMID: 37066213 PMCID: PMC10104178 DOI: 10.1101/2023.04.08.23288321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Background Tracking the emergence and spread of antimalarial drug resistance has become critical to sustaining progress towards the control and eventual elimination of malaria in South Asia, especially India. Methods An amplicon sequencing protocol was used for high-throughput molecular surveillance of antimalarial drug resistance in a total of 158 isolates at three sites in India: Chennai, Nadiad and Rourkela. Five genes of the Plasmodium falciparum implicated in antimalarial resistance were investigated here; Pfcrt for chloroquine resistance, Pfdhfr for pyrimethamine resistance, Pfdhps for sulfadoxine resistance, Pfk13 for artemisinin resistance and Pfmdr1 for resistance to multiple antimalarials. Results Mutations in the propeller domain of PfK13 were observed in two samples only, however these mutations are not validated for artemisinin resistance. A high proportion of parasites from the P. falciparum dominant site Rourkela showed wild-type Pfcrt and Pfdhfr haplotypes, while mutant Pfcrt and Pfdhfr haplotypes were fixed at the P. vivax dominant sites Chennai and Nadiad. The wild-type PfDHPS haplotype was predominant across all study sites. Finally, we observed the largest proportion of suspected multi-clonal infections at Rourkela, which has the highest transmission of P. falciparum among our study sites. Conclusion This is the first simultaneous high-throughput next generation sequencing of five complete P. falciparum genes from infected patients in India.
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Affiliation(s)
- Sonal Kale
- National Institute of Malaria Research, Indian Council of Medical Research, Sector 8, Dwarka, New Delhi, India
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland, USA
| | - Swapna M. Uplekar
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Nabamita Bandyopadhyay
- National Institute of Malaria Research, Indian Council of Medical Research, Sector 8, Dwarka, New Delhi, India
| | - Pavitra N. Rao
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Syed Z. Ali
- National Institute of Malaria Research Field Unit, Sector 1 Health Center, Rourkela, Odisha, India
| | - S.K. Sharma
- National Institute of Malaria Research Field Unit, Sector 1 Health Center, Rourkela, Odisha, India
| | - Nikunj Tandel
- National Institute of Malaria Research Field Unit, Civil Hospital, Nadiad, Gujarat, India
| | - Ankita Patel
- National Institute of Malaria Research Field Unit, Civil Hospital, Nadiad, Gujarat, India
| | - Ranvir Singh
- National Institute of Malaria Research Field Unit, Civil Hospital, Nadiad, Gujarat, India
| | - Aaron Dank
- National Institute of Malaria Research Field Unit, Civil Hospital, Nadiad, Gujarat, India
| | - Sangamithra Ravishankaran
- National Institute of Malaria Research Field Unit, Indian Council of Medical Research, National Institute of Epidemiology Campus, Ayapakkam, Chennai, Tamil Nadu, India
| | - G Sri Lakshmi Priya
- National Institute of Malaria Research Field Unit, Indian Council of Medical Research, National Institute of Epidemiology Campus, Ayapakkam, Chennai, Tamil Nadu, India
| | - Aswin Asokan
- National Institute of Malaria Research Field Unit, Indian Council of Medical Research, National Institute of Epidemiology Campus, Ayapakkam, Chennai, Tamil Nadu, India
| | - Alex Eapen
- National Institute of Malaria Research Field Unit, Indian Council of Medical Research, National Institute of Epidemiology Campus, Ayapakkam, Chennai, Tamil Nadu, India
| | - Om. P. Singh
- National Institute of Malaria Research, Indian Council of Medical Research, Sector 8, Dwarka, New Delhi, India
| | - Jane M. Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Prashant K. Mallick
- National Institute of Malaria Research, Indian Council of Medical Research, Sector 8, Dwarka, New Delhi, India
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Shetty AC, Jacob CG, Huang F, Li Y, Agrawal S, Saunders DL, Lon C, Fukuda MM, Ringwald P, Ashley EA, Han KT, Hlaing TM, Nyunt MM, Silva JC, Stewart KE, Plowe CV, O'Connor TD, Takala-Harrison S. Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns. Nat Commun 2019; 10:2665. [PMID: 31209259 PMCID: PMC6572796 DOI: 10.1038/s41467-019-10121-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 04/17/2019] [Indexed: 02/08/2023] Open
Abstract
Estimates of Plasmodium falciparum migration may inform strategies for malaria elimination. Here we elucidate fine-scale parasite population structure and infer recent migration across Southeast Asia using identity-by-descent (IBD) approaches based on genome-wide single nucleotide polymorphisms called in 1722 samples from 54 districts. IBD estimates are consistent with isolation-by-distance. We observe greater sharing of larger IBD segments between artemisinin-resistant parasites versus sensitive parasites, which is consistent with the recent spread of drug resistance. Our IBD analyses reveal actionable patterns, including isolated parasite populations, which may be prioritized for malaria elimination, as well as asymmetrical migration identifying potential sources and sinks of migrating parasites.
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Affiliation(s)
- Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Graduate Program in Epidemiology and Human Genetics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | | | - Fang Huang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China
| | - Yao Li
- Center for Geospatial Information Science, University of Maryland, College Park, MD, 20742, USA
| | - Sonia Agrawal
- Graduate Program in Epidemiology and Human Genetics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David L Saunders
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Chanthap Lon
- Armed Forces Research Institute of Medical Sciences, Khan Daun Penh, Phnom Penh, Cambodia
| | - Mark M Fukuda
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Pascal Ringwald
- Global Malaria Programme, World Health Organization, Geneva, 1202, Switzerland
| | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Kay Thwe Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, 11191, Myanmar
| | | | - Myaing M Nyunt
- Duke Global Health Institute, Duke University, Durham, NC, 27710, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Kathleen E Stewart
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | | | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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Kar NP, Chauhan K, Nanda N, Kumar A, Carlton JM, Das A. Comparative assessment on the prevalence of mutations in the Plasmodium falciparum drug-resistant genes in two different ecotypes of Odisha state, India. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 41:47-55. [PMID: 26988711 PMCID: PMC4868809 DOI: 10.1016/j.meegid.2016.03.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/11/2016] [Accepted: 03/12/2016] [Indexed: 01/14/2023]
Abstract
Considering malaria as a local and focal disease, epidemiological understanding of different ecotypes of malaria can help in devising novel control measures. One of the major hurdles in malaria control lies on the evolution and dispersal of the drug-resistant malaria parasite, Plasmodium falciparum. We herewith present data on genetic variation at the Single Nucleotide Polymorphism (SNP) level in four different genes of P. falciparum (Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps) that confer resistance to different antimalarials in two different eco-epidemiological settings, i.e. Hilly-Forest (HF) and Riverine-Plain (RP), in a high malaria endemic district of Odisha state, India. Greater frequency of antimalarial resistance conferring SNPs and haplotypes was observed in all four genes in P. falciparum, and Pfdhps was the most variable gene among the four. No significant genetic differentiation could be observed in isolates from HF and RP ecotypes. Twelve novel, hitherto unreported nucleotide mutations could be observed in the Pfmdr1 and Pfdhps genes. While the Pfdhps gene presented highest haplotype diversity, the Pfcrt gene displayed the highest nucleotide diversity. When the data on all the four genes were complied, the isolates from HF ecotype were found to harbour higher average nucleotide diversity than those coming from RP ecotype. High and positive Tajima's D values were obtained for the Pfcrt and Pfdhfr genes in isolates from both the HF and RP ecotypes, with statistically significant deviation from neutrality in the RP ecotype. Different patterns of Linkage Disequilibrium (LD) among SNPs located in different drug-resistant genes were found in the isolates collected from HF and RP ecotypes. Whereas in the HF ecotype, SNPs in the Pfmdr1 and Pfdhfr were significantly associated, in the RP ecotype, SNPs located in Pfcrt were associated with Pfmdr1, Pfdhfr and Pfdhps. These findings provide a baseline understanding on how different micro eco-epidemiological settings influence evolution and spread of different drug resistance alleles. Our findings further suggest that drug resistance to chloroquine and sulfadoxine-pyrimethamine is approaching fixation level, which requires urgent attention of malaria control programme in India.
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Affiliation(s)
- Narayani Prasad Kar
- National Institute of Malaria Research, Indian Council of Medical Research, Sector-8, Dwarka, New Delhi-110077, India
| | - Kshipra Chauhan
- National Institute of Malaria Research, Indian Council of Medical Research, Sector-8, Dwarka, New Delhi-110077, India
| | - Nutan Nanda
- National Institute of Malaria Research, Indian Council of Medical Research, Sector-8, Dwarka, New Delhi-110077, India
| | - Ashwani Kumar
- National Institute of Malaria Research, DHS Building, Campal, Panaji, Field Unit, Goa-403001, India
| | - Jane M. Carlton
- Department of Biology, New York University, 12 Waverly Place, New York, NY 10009, U.S.A
| | - Aparup Das
- National Institute of Malaria Research, Indian Council of Medical Research, Sector-8, Dwarka, New Delhi-110077, India
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A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India. J Clin Microbiol 2016; 54:1500-1511. [PMID: 27008882 PMCID: PMC4879288 DOI: 10.1128/jcm.00235-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/20/2016] [Indexed: 11/20/2022] Open
Abstract
A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of six Plasmodium falciparum genes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverse P. falciparum reference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy.
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Sharma D, Lather M, Mallick PK, Adak T, Dang AS, Valecha N, Singh OP. Polymorphism in drug resistance genes dihydrofolate reductase and dihydropteroate synthase in Plasmodium falciparum in some states of India. Parasit Vectors 2015; 8:471. [PMID: 26381498 PMCID: PMC4574150 DOI: 10.1186/s13071-015-1080-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sulfadoxine-pyrimethamine (SP) combination drug is currently being used in India for the treatment of Plasmodium falciparum as partner drug in artemisinin-based combination therapy (ACT). Resistance to sulfadoxine and pyrimethamine in P. falciparum is linked with mutations in dihydropteroate synthase (pfdhps) and dihydrofolate reductase (pfdhfr) genes respectively. This study was undertaken to estimate the prevalence of such mutations in pfdhfr and pfdhps genes in four states of India. METHODS Plasmodium falciparum isolates were collected from two states of India with high malaria incidence i.e., Jharkhand and Odisha and two states with low malaria incidence i.e., Andhra Pradesh and Uttar Pradesh between years 2006 to 2012. Part of sulfadoxine-pyrimethamine (SP) drug resistance genes, pfdhfr and pfdhps were PCR-amplified, sequenced and analyzed. RESULTS A total of 217 confirmed P. falciparum isolates were sequenced for both Pfdhfr and pfdhps gene. Two pfdhfr mutations 59R and 108N were most common mutations prevalent in all localities in 77 % of isolates. Additionally, I164L was found in Odisha and Jharkhand only (4/70 and 8/84, respectively). Another mutation 51I was found in Odisha only (3/70). The pfdhps mutations 436A, 437G, 540E and 581G were found in Jharkhand and Odisha only in 13, 26, 14 and 13 % isolates respectively, and was absent in Uttar Pradesh and Andhra Pradesh. Combined together for pfdhps and pfdhfr locus, triple, quadruple, quintuple and sextuple mutations were present in Jharkhand and Odisha while absent in Uttar Pradesh and Andhra Pradesh. CONCLUSION While only double mutants of pfdhfr was present in low transmission area (Uttar Pradesh and Andhra Pradesh) with total absence of pfdhps mutants, up to sextuple mutations were present in high transmission areas (Odisha and Jharkhand) for both the genes combined. Presence of multiple mutations in pfdhfr and pfdhps genes linked to SP resistance in high transmission area may lead to fixation of multiple mutations in presence of high drug pressure and high recombination rate.
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Affiliation(s)
- Divya Sharma
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi-110077, India.
| | - Manila Lather
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi-110077, India.
| | - Prashant K Mallick
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi-110077, India.
| | - Tridibes Adak
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi-110077, India.
| | - Amita S Dang
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India.
| | - Neena Valecha
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi-110077, India.
| | - Om P Singh
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi-110077, India.
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Manrique P, Hoshi M, Fasabi M, Nolasco O, Yori P, Calderón M, Gilman RH, Kosek MN, Vinetz JM, Gamboa D. Assessment of an automated capillary system for Plasmodium vivax microsatellite genotyping. Malar J 2015; 14:326. [PMID: 26293655 PMCID: PMC4546211 DOI: 10.1186/s12936-015-0842-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several platforms have been used to generate the primary data for microsatellite analysis of malaria parasite genotypes. Each has relative advantages but share a limitation of being time- and cost-intensive. A commercially available automated capillary gel cartridge system was assessed in the microsatellite analysis of Plasmodium vivax diversity in the Peruvian Amazon. METHODS The reproducibility and accuracy of a commercially-available automated capillary system, QIAxcel, was assessed using a sequenced PCR product of 227 base pairs. This product was measured 42 times, then 27 P. vivax samples from Peruvian Amazon subjects were analyzed with this instrument using five informative microsatellites. Results from the QIAxcel system were compared with a Sanger-type sequencing machine, the ABI PRISM(®) 3100 Genetic Analyzer. RESULTS Significant differences were seen between the sequenced amplicons and the results from the QIAxcel instrument. Different runs, plates and cartridges yielded significantly different results. Additionally, allele size decreased with each run by 0.045, or 1 bp, every three plates. QIAxcel and ABI PRISM systems differed in giving different values than those obtained by ABI PRISM, and too many (i.e. inaccurate) alleles per locus were also seen with the automated instrument. CONCLUSIONS While P. vivax diversity could generally be estimated using an automated capillary gel cartridge system, the data demonstrate that this system is not sufficiently precise for reliably identifying parasite strains via microsatellite analysis. This conclusion reached after systematic analysis was due both to inadequate precision and poor reproducibility in measuring PCR product size.
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Affiliation(s)
- Paulo Manrique
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Mari Hoshi
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | | | - Oscar Nolasco
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Pablo Yori
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, MD, USA.
| | - Martiza Calderón
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Robert H Gilman
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, MD, USA.
| | - Margaret N Kosek
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, MD, USA.
| | - Joseph M Vinetz
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru. .,Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Dionicia Gamboa
- Malaria Laboratory, Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru. .,Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia, Lima, Peru.
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Tyagi S, Das A. Mitochondrial population genomic analyses reveal population structure and demography of Indian Plasmodium falciparum. Mitochondrion 2015; 24:9-21. [PMID: 26149324 DOI: 10.1016/j.mito.2015.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 06/29/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022]
Abstract
Inference on the genetic diversity of Plasmodium falciparum populations could help in better management of malaria. A very recent study with mitochondrial (mt) genomes in global P. falciparum had revealed interesting evolutionary genetic patterns of Indian isolates in comparison to global ones. However, no population genetic study using the whole mt genome sequences of P. falciparum isolates collected in the entire distribution range in India has yet been performed. We herewith have analyzed 85 whole mt genomes (48 already published and 37 entirely new) sampled from eight differentially endemic Indian locations to estimate genetic diversity and infer population structure and historical demography of Indian P. falciparum. We found 19 novel Indian-specific Single Nucleotide Polymorphisms (SNPs) and 22 novel haplotypes segregating in Indian P. falciparum. Accordingly, high haplotype and nucleotide diversities were detected in Indian P. falciparum in comparison to many other global isolates. Indian P. falciparum populations were found to be moderately sub-structured with four different genetic clusters. Interestingly, group of local populations aggregate to form each cluster; while samples from Jharkhand and Odisha formed a single cluster, P. falciparum isolates from Asom formed an independent one. Similarly, Surat, Bilaspur and Betul formed a single cluster and Goa and Mangalore formed another. Interestingly, P. falciparum isolates from the two later populations were significantly genetically differentiated from isolates collected in other six Indian locations. Signature of historical population expansion was evident in five population samples, and the onset of expansion event was found to be very similar to African P. falciparum. In agreement with the previous finding, the estimated Time to Most Recent Common Ancestor (TMRCA) and the effective population size were high in Indian P. falciparum. All these genetic features of Indian P. falciparum with high mt genome diversity are somehow similar to Africa, but quite different from other Asian population samples.
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Affiliation(s)
- Suchi Tyagi
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, New Delhi, India
| | - Aparup Das
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, New Delhi, India.
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Awasthi G, Das A. Genetics of chloroquine-resistant malaria: a haplotypic view. Mem Inst Oswaldo Cruz 2015; 108:947-61. [PMID: 24402147 PMCID: PMC4005552 DOI: 10.1590/0074-0276130274] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 09/26/2013] [Indexed: 02/05/2023] Open
Abstract
The development and rapid spread of chloroquine resistance (CQR) in
Plasmodium falciparum have triggered the identification of
several genetic target(s) in the P. falciparum genome. In
particular, mutations in the Pfcrt gene, specifically, K76T and
mutations in three other amino acids in the region adjoining K76 (residues 72, 74, 75
and 76), are considered to be highly related to CQR. These various mutations form
several different haplotypes and Pfcrt gene polymorphisms and the
global distribution of the different CQR- Pfcrt haplotypes in
endemic and non-endemic regions of P. falciparum malaria have been
the subject of extensive study. Despite the fact that the Pfcrt gene
is considered to be the primary CQR gene in P. falciparum , several
studies have suggested that this may not be the case. Furthermore, there is a poor
correlation between the evolutionary implications of the Pfcrt
haplotypes and the inferred migration of CQR P. falciparum based on
CQR epidemiological surveillance data. The present paper aims to clarify the existing
knowledge on the genetic basis of the different CQR- Pfcrt
haplotypes that are prevalent in worldwide populations based on the published
literature and to analyse the data to generate hypotheses on the genetics and
evolution of CQR malaria.
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Asare KK, Boampong JN, Afoakwah R, Ameyaw EO, Sehgal R, Quashie NB. Use of proscribed chloroquine is associated with an increased risk of pfcrt T76 mutation in some parts of Ghana. Malar J 2014; 13:246. [PMID: 24969960 PMCID: PMC4088365 DOI: 10.1186/1475-2875-13-246] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 06/19/2014] [Indexed: 01/18/2023] Open
Abstract
Background After years of disuse of chloroquine (CQ) as first-line anti-malarial drug in Ghana, reports from molecular studies conducted in parts of the country indicate varying prevalence of T76 mutation in the pfcrt gene. This situation has several health implications, one being that mutations that confer resistance to CQ have been reported to show substantial cross-resistance to other anti-malarial drugs. It is important to identify some of the factors contributing to the continuous presence of CQ resistance markers in the country. This study determined the prevalence of T76 mutation in pfcrt gene of Plasmodium falciparum isolates collected from selected areas of the Central region of Ghana and correlated with the level of CQ use in these areas. Methods Plasmodium falciparum DNA was extracted from collected blood-blot filter paper samples in the study sites. The prevalence of T76 point mutation in pfcrt gene was assessed using nested PCR followed by RFLP. CQ from pharmacy and chemical shops was obtained using mystery buying method. The extent of CQ use by the participants was determined by measuring the level of the drug in their urine samples using the Saker-Solomon method. Results Of the 214 P. falciparum isolates analysed, 71.9% were found to have T76 mutation of pfcrt gene. The study revealed that 14.49% of community pharmacies and chemical shops had stocks of CQ for sale while 16.9% of the participants had CQ in their urine samples. There is five times more risks of becoming infected with CQ resistant strain for staying in an area where CQ is stocked for sale [RR = 0.20, p < 0.0001] and thirteen times more risks of having CQ-resistant mutant from those who still use CQ than non-users [OR = 0.08, p < 0.0001]. Conclusion This study has shown that high variation in the prevalence of T76 mutations of P. falciparum is linked with the level of CQ stocking and usage within study area.
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Affiliation(s)
| | - Johnson N Boampong
- Department of Biomedical and Forensic Sciences, University of Cape Coast, Cape Coast, Ghana.
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10
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Tyagi S, Pande V, Das A. New insights into the evolutionary history of Plasmodium falciparum from mitochondrial genome sequence analyses of Indian isolates. Mol Ecol 2014; 23:2975-87. [PMID: 24845521 DOI: 10.1111/mec.12800] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 05/16/2014] [Accepted: 05/16/2014] [Indexed: 12/31/2022]
Abstract
Estimating genetic diversity and inferring the evolutionary history of Plasmodium falciparum could be helpful in understanding origin and spread of virulent and drug-resistant forms of the malaria pathogen and therefore contribute to malaria control programme. Genetic diversity of the whole mitochondrial (mt) genome of P. falciparum sampled across the major distribution ranges had been reported, but no Indian P. falciparum isolate had been analysed so far, even though India is highly endemic to P. falciparum malaria. We have sequenced the whole mt genome of 44 Indian field isolates and utilized published data set of 96 genome sequences to present global genetic diversity and to revisit the evolutionary history of P. falciparum. Indian P. falciparum presents high genetic diversity with several characteristics of ancestral populations and shares many of the genetic features with African and to some extent Papua New Guinean (PNG) isolates. Similar to African isolates, Indian P. falciparum populations have maintained high effective population size and undergone rapid expansion in the past with oldest time to the most recent common ancestor (TMRCA). Interestingly, one of the four single nucleotide polymorphisms (SNPs) that differentiates P. falciparum from P. falciparum-like isolates (infecting non-human primates in Africa) was found to be segregating in five Indian P. falciparum isolates. This SNP was in tight linkage with other two novel SNPs that were found exclusively in these five Indian isolates. The results on the mt genome sequence analyses of Indian isolates on the whole add to the current understanding on the evolutionary history of P. falciparum.
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Affiliation(s)
- Suchi Tyagi
- Evolutionary Genomics and Bioinformatics Laboratory, National Institute of Malaria Research, Sector - 8 Dwarka, New Delhi, 110077, India
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Sutton PL. A call to arms: on refining Plasmodium vivax microsatellite marker panels for comparing global diversity. Malar J 2013; 12:447. [PMID: 24330329 PMCID: PMC3878832 DOI: 10.1186/1475-2875-12-447] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 12/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microsatellite (MS) markers have become an important tool for studying the population diversity, evolutionary history and multiplicity of infection (MOI) of malaria parasite infections. MS are typically selected on the basis of being highly polymorphic. However, it is known that the polymorphic potential (mutability) of each marker can vary as much as two orders of magnitude, which radically changes how diversity is represented in the genome from one marker to the next. Over the past decade, approximately 240 Plasmodium vivax MS have been published, comprising nine major panels of markers. Inconsistent usage of each panel has resulted in a surfeit of descriptive genetic diversity data that are largely incomparable between populations. The objective of this study was to statistically evaluate the quality of individual MS markers in order to validate a refined panel of markers that will provide a balanced picture of P. vivax population diversity. METHODS All previously published data, including genetic diversity indices, MS parameters, and population parameters, were assembled from 18 different global studies into a flat file to facilitate statistical analysis and modelling using JMP® Genomics 6.0 (SAS Institute Inc, Cary, NC, USA). Statistical modeling was employed to down-select markers with extreme variation among the mean number of alleles, expected heterozygosity, maximum repeat length and/or chromosomal location of the repeat. Individual MS were analysed by step-down whole model linear regression and standard least squares fit models, both stratified by annual parasite incidence to identify MS markers with values significantly different from the mean. RESULTS Of the 42 MS under evaluation in this study, 18 (nine high priority) were identified as ideal candidates for measuring population diversity between global regions, while five (two high priority) additional markers were identified as candidates for MOI studies. CONCLUSIONS MS diversity was found to be a function of endemicity and motif structure. Evaluation of individual MS permitted the assembly of a refined panel of markers that can be reliably utilized in the field to compare population structures between global regions.
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Affiliation(s)
- Patrick L Sutton
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
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Mallick PK, Singh R, Singh OP, Singh AK, Bhasin VK, Valecha N. Reduced heterozygosity at intragenic and flanking microsatellites of pfcrt gene establishes natural selection based molecular evolution of chloroquine-resistant Plasmodium falciparum in India. INFECTION GENETICS AND EVOLUTION 2013; 20:407-12. [DOI: 10.1016/j.meegid.2013.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/24/2013] [Accepted: 10/01/2013] [Indexed: 11/26/2022]
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Chauhan K, Pande V, Das A. Analyses of genetic variations at microsatellite loci present in-and-around the Pfcrt gene in Indian Plasmodium falciparum. INFECTION GENETICS AND EVOLUTION 2013; 20:476-87. [PMID: 24157593 DOI: 10.1016/j.meegid.2013.10.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/10/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
Abstract
Evolution and spread of chloroquine resistant (CQR) malaria parasite Plasmodium falciparum have posed great threat in malaria intervention across the globe. The occurrence of K76T mutation in the P. falciparum chloroquine resistance transporter (pfcrt) gene has been widely attributed to CQR with four neighboring mutations providing compensatory fitness benefit to the parasite survival. Understanding evolutionary patterns of the pfcrt gene is of great relevance not only for devising new malaria control measures but also could serve as a model to understand evolution and spread of other human drug-resistant pathogens. Several studies, mainly based on differential patterns of diversities of the microsatellite loci placed in-and-around the pfcrt gene have indicated the role of positive natural selection under the 'hitchhiking' model of molecular evolution. However, the studies were restricted to limited number of microsatellite loci present inside the pfcrt gene. Moreover, comparatively higher level of diversities in microsatellite loci present inside the pfcrt gene than the loci flanking the pfcrt gene are hallmarks of Indian P. falciparum, presenting contrasting evolutionary models to global isolates. With a view to infer evolutionary patterns of the pfcrt gene in Indian P. falciparum, we have adopted a unique sampling scheme of two types of populations (cultured and field collected) and utilized 20 polymorphic microsatellite loci (16 located inside the pfcrt gene and four in the two flanking regions) to disentangle between genetic drift (inbred cultured isolates) and natural selection (field isolates). Data analyses employing different population genetic tests could not straightforwardly explain either the model invoking 'genetic hitchhiking' or 'genetic drift'. However, complex evolutionary models influenced by both demography and natural selection or an alternative model of natural selection (e.g. diversifying/balancing selection) might better explain the observed microsatellite variation in-and-around the pfcrt gene in Indian P. falciparum.
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Affiliation(s)
- Kshipra Chauhan
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector 8, Dwarka, New Delhi 110077, India
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