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Early AM, Daniels RF, Farrell TM, Grimsby J, Volkman SK, Wirth DF, MacInnis BL, Neafsey DE. Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing. Malar J 2019; 18:219. [PMID: 31262308 PMCID: PMC6604269 DOI: 10.1186/s12936-019-2856-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deep sequencing of targeted genomic regions is becoming a common tool for understanding the dynamics and complexity of Plasmodium infections, but its lower limit of detection is currently unknown. Here, a new amplicon analysis tool, the Parallel Amplicon Sequencing Error Correction (PASEC) pipeline, is used to evaluate the performance of amplicon sequencing on low-density Plasmodium DNA samples. Illumina-based sequencing of two Plasmodium falciparum genomic regions (CSP and SERA2) was performed on two types of samples: in vitro DNA mixtures mimicking low-density infections (1-200 genomes/μl) and extracted blood spots from a combination of symptomatic and asymptomatic individuals (44-653,080 parasites/μl). Three additional analysis tools-DADA2, HaplotypR, and SeekDeep-were applied to both datasets and the precision and sensitivity of each tool were evaluated. RESULTS Amplicon sequencing can contend with low-density samples, showing reasonable detection accuracy down to a concentration of 5 Plasmodium genomes/μl. Due to increased stochasticity and background noise, however, all four tools showed reduced sensitivity and precision on samples with very low parasitaemia (< 5 copies/μl) or low read count (< 100 reads per amplicon). PASEC could distinguish major from minor haplotypes with an accuracy of 90% in samples with at least 30 Plasmodium genomes/μl, but only 61% at low Plasmodium concentrations (< 5 genomes/μl) and 46% at very low read counts (< 25 reads per amplicon). The four tools were additionally used on a panel of extracted parasite-positive blood spots from natural malaria infections. While all four identified concordant patterns of complexity of infection (COI) across four sub-Saharan African countries, COI values obtained for individual samples differed in some cases. CONCLUSIONS Amplicon deep sequencing can be used to determine the complexity and diversity of low-density Plasmodium infections. Despite differences in their approach, four state-of-the-art tools resolved known haplotype mixtures with similar sensitivity and precision. Researchers can therefore choose from multiple robust approaches for analysing amplicon data, however, error filtration approaches should not be uniformly applied across samples of varying parasitaemia. Samples with very low parasitaemia and very low read count have higher false positive rates and call for read count thresholds that are higher than current default recommendations.
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Affiliation(s)
- Angela M Early
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Rachel F Daniels
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Timothy M Farrell
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jonna Grimsby
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sarah K Volkman
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- College of Natural, Behavioral, and Health Sciences, Simmons University, Boston, MA, 02115, USA
| | - Dyann F Wirth
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Bronwyn L MacInnis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Daniel E Neafsey
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
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Ghoshal S, Gajendra P, Datta Kanjilal S, Mitra M, Sengupta S. Diversity analysis of MSP1 identifies conserved epitope organization in block 2 amidst high sequence variability in Indian Plasmodium falciparum isolates. Malar J 2018; 17:447. [PMID: 30509263 PMCID: PMC6276175 DOI: 10.1186/s12936-018-2592-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 11/23/2018] [Indexed: 02/02/2023] Open
Abstract
Background Despite its immunogenicity, the polymorphic nature of merozoite surface protein 1, an important vaccine candidate for Plasmodium falciparum malaria, remains a concern. This study analyses the impact of genetic variability and parasite population structure on epitope organization of different MSP1 segments. Methods Altogether 98 blood samples collected from P. falciparum infected mild and severe malaria patients of Chhattisgarh and West Bengal were used to sequence regions encoding block 2 and MSP1-19 of msp1. Sequences were analysed using MEGA7, DnaSPv5, Arlequin3.5 and BepiPred. Results All three major MSP1 block 2 allele families namely K1, MAD20 and RO33 were detected in the samples and they together resulted in 41 indel variants. Chhattisgarh samples displayed an average MOI of 2.07 ± 1.59 which was higher in mild malaria and in age group < 18 years. Ultra-structure of block 2 alleles revealed that mutation and repeat expansion were two major mechanisms responsible for allelic variability of K1 and MAD20. Regions flanking block 2 were highly variable in Chhattisgarh with average mismatch differences (k) ranging from 1.198 to 5.156 for three families. In contrast, region encompassing MSP1-19 exhibited limited heterogeneity (kChhattisgarh = 1.45, kWest Bengal = 1.363). Of the 50 possible B cell linear epitopes predicted from block 2 variants, 94.9% (131 of 138) of the parasites could be represented by three conserved antigens. Conclusions Present data indicates that natural selection and transmission intensity jointly play a role in controlling allelic diversity of MSP1 in Indian parasite isolates. Despite remarkable genetic variability, a limited number of predominant and conserved epitopes are present in Indian parasite isolates reinstating the importance of MSP1 as a promising malaria vaccine candidate. Electronic supplementary material The online version of this article (10.1186/s12936-018-2592-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sharmistha Ghoshal
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700 019, India
| | - Pragya Gajendra
- School of Studies in Anthropology, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, 492010, India
| | - Sumana Datta Kanjilal
- Department of Pediatric Medicine, Institute of Post Graduate Medical Education & Research, Kolkata, West Bengal, India
| | - Mitashree Mitra
- School of Studies in Anthropology, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, 492010, India
| | - Sanghamitra Sengupta
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700 019, India.
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Mohammed H, Kassa M, Mekete K, Assefa A, Taye G, Commons RJ. Genetic diversity of the msp-1, msp-2, and glurp genes of Plasmodium falciparum isolates in Northwest Ethiopia. Malar J 2018; 17:386. [PMID: 30359280 PMCID: PMC6203214 DOI: 10.1186/s12936-018-2540-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/20/2018] [Indexed: 11/30/2022] Open
Abstract
Background Determination of the genetic diversity of malaria parasites can inform the intensity of transmission and identify potential deficiencies in malaria control programmes. This study was conducted to characterize the genetic diversity and allele frequencies of Plasmodium falciparum in Northwest Ethiopia along the Eritrea and Sudan border. Methods A total of 90 isolates from patients presenting to the local health centre with uncomplicated P. falciparum were collected from October 2014 to January 2015. DNA was extracted and the polymorphic regions of the msp-1, msp-2 and glurp loci were genotyped by nested polymerase chain reactions followed by gel electrophoresis for fragment analysis. Results Allelic variation in msp-1, msp-2 and glurp were identified in 90 blood samples. A total of 34 msp alleles (12 for msp-1 and 22 for msp-2) were detected. For msp-1 97.8% (88/90), msp-2 82.2% (74/90) and glurp 46.7% (42/90) were detected. In msp-1, MAD20 was the predominant allelic family detected in 47.7% (42/88) of the isolates followed by RO33 and K1. For msp-2, the frequency of FC27 and IC/3D7 were 77% (57/74) and 76% (56/74), respectively. Nine glurp RII region genotypes were identified. Seventy percent of isolates had multiple genotypes and the overall mean multiplicity of infection was 2.6 (95% CI 2.25–2.97). The heterozygosity index was 0.82, 0.62 and 0.20 for msp-1, msp-2 and glurp, respectively. There was no significant association between multiplicity of infection and age or parasite density. Conclusions There was a high degree of genetic diversity with multiple clones in P. falciparum isolates from Northwest Ethiopia suggesting that there is a need for improved malaria control efforts in this region. Electronic supplementary material The online version of this article (10.1186/s12936-018-2540-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hussein Mohammed
- Malaria, Neglected Tropical Diseases Research Team Bacterial, Parasitic, Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
| | - Moges Kassa
- Malaria, Neglected Tropical Diseases Research Team Bacterial, Parasitic, Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Kalkidan Mekete
- Malaria, Neglected Tropical Diseases Research Team Bacterial, Parasitic, Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Ashenafi Assefa
- Malaria, Neglected Tropical Diseases Research Team Bacterial, Parasitic, Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Girum Taye
- Malaria, Neglected Tropical Diseases Research Team Bacterial, Parasitic, Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Robert J Commons
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia
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Soe TN, Wu Y, Tun MW, Xu X, Hu Y, Ruan Y, Win AYN, Nyunt MH, Mon NCN, Han KT, Aye KM, Morris J, Su P, Yang Z, Kyaw MP, Cui L. Genetic diversity of Plasmodium falciparum populations in southeast and western Myanmar. Parasit Vectors 2017; 10:322. [PMID: 28676097 PMCID: PMC5496439 DOI: 10.1186/s13071-017-2254-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/19/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genetic diversity of malaria parasites reflects the complexity and size of the parasite populations. This study was designed to explore the genetic diversity of Plasmodium falciparum populations collected from two southeastern areas (Shwekyin and Myawaddy bordering Thailand) and one western area (Kyauktaw bordering Bangladesh) of Myanmar. METHODS A total of 267 blood samples collected from patients with acute P. falciparum infections during 2009 and 2010 were used for genotyping at the merozoite surface protein 1 (Msp1), Msp2 and glutamate-rich protein (Glurp) loci. RESULTS One hundred and eighty four samples were successfully genotyped at three genes. The allelic distributions of the three genes were all significantly different among three areas. MAD20 and 3D7 were the most prevalent alleles in three areas for Msp1 and Msp2, respectively. The Glurp allele with a bin size of 700-750 bp was the most prevalent both in Shwekyin and Myawaddy, whereas two alleles with bin sizes of 800-850 bp and 900-1000 bp were the most prevalent in the western site Kyauktaw. Overall, 73.91% of samples contained multiclonal infections, resulting in a mean multiplicity of infection (MOI) of 1.94. Interestingly, the MOI level presented a rising trend with the order of Myawaddy, Kyauktaw and Shwekyin, which also paralleled with the increasing frequencies of Msp1 RO33 and Msp2 FC27 200-250 bp alleles. Msp1 and Msp2 genes displayed higher levels of diversity and higher MOI rates than Glurp. PCR revealed four samples (two from Shwekyin and two from Myawaddy) with mixed infections of P. falciparum and P. vivax. CONCLUSIONS This study genotyped parasite clinical samples from two southeast regions and one western state of Myanmar at the Msp1, Msp2 and Glurp loci, which revealed high levels of genetic diversity and mixed-strain infections of P. falciparum populations at these sites. The results indicated that malaria transmission intensity in these regions remained high and more strengthened control efforts are needed. The genotypic data provided baseline information for monitoring the impacts of malaria elimination efforts in the region.
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Affiliation(s)
- Than Naing Soe
- Department of Public Health, Ministry of Health and Sports, Nay Pyi Taw, Myanmar
| | - Yanrui Wu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China.,Department of Cell Biology & Genetics, Kunming Medical University, Kunming, China
| | - Myo Win Tun
- Department of Medical Research, Yangon city, Myanmar
| | - Xin Xu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yue Hu
- Department of Pathology, Kunming Medical University, Kunming, China
| | - Yonghua Ruan
- Department of Pathology, Kunming Medical University, Kunming, China
| | | | | | | | - Kay Thwe Han
- Department of Medical Research, Yangon city, Myanmar
| | - Khin Myo Aye
- Department of Medical Research, Yangon city, Myanmar
| | - James Morris
- Department of Genetics and Biochemistry, Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC, USA
| | - Pincan Su
- Transfusion Medicine Research Department, Yunnan Kunming Blood Center, Kunming, China
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China.
| | - Myat Phone Kyaw
- Department of Medical Research, Yangon city, Myanmar. .,Myanmar Medical Association, Yangon, Myanmar.
| | - Liwang Cui
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China. .,Department of Entomology, Pennsylvania State University, University Park city, PA, 16802, USA.
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