Dr Olivo Miotto

Research Area: Global Health
Technology Exchange: Bioinformatics, Computational biology, SNP typing and Statistical genetics
Scientific Themes: Genetics & Genomics and Tropical Medicine & Global Health
Keywords: genomics, informatics, malaria, epidemiology, infectious disease and software
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Because of malaria, millions of African children die before their first day at school. For decades, scientists and health authorities have raised hopes of eliminating this burden on the developing world, only to have these hopes dashed, time after time, by the astonishing adaptability of Plasmodium parasites, which seem capable of becoming tolerant to most drugs we deploy. Today, genomic technologies provide a powerful new weapon against these parasites. At the Centre for Genomics and Global Health, we have developed methods for determining the genetic code of Plasmodium parasite directly from blood samples taken from infected patients. Thanks to the falling cost of sequencing, and the reliability of our approach, we are now able to sequence literally thousands of parasites from clinical cases, and map this genomic information in geographical, ecological and historical contexts. Our goal is to determine how parasite populations change as a result of human intervention and environmental change, and observe new epidemiological trends in real time, to inform and guide public health intervention. In other words, "genomic epidemiology" will monitor Plasmodium evolution, so that humanity can keep steps ahead of the parasite.

Olivo Miotto focuses on translating the massive quantities of data produced by sequencing thousands of genomes into meaningful knowledge about the epidemiology of Plasmodium falciparum. By analyzing hundreds of thousands of genomic variations in each blood sample, he studies the genetics of parasite populations in four continents, and identifies patterns of evolution associated to responses to drug pressure and other human interventions. Based in Bangkok, Olivo collaborates with many clinical research groups in malaria endemic regions, particularly in Southeast Asia, to study relationships between  response to clinical therapy and genetics of the disease-causing parasites in the patient. In the early stages, the focus is on immediate problems, such as discovering mutations causing resistance to current drugs, such as artemisinin. However, Olivo's longer-term perspective is to create tools that will identify patterns in thousands of accumulated genomic sequences, leading to a deep understanding of parasite evolution and, ultimately, to interventions that will win the struggle against the disease.

When learning about Darwin at age 12, Olivo thought evolution was the coolest thing he had heard of. It took him decades to realize that it was also the best use for his skills. In between, he studied physics and worked as a software engineer, both in the commercial and academic worlds. At various times he focussed on Web applications, graphical user  interfaces, speech synthesis, online learning, and database systems, before finally switching to bioinformatics and genomics.

Name Department Institution Country
Prof Nicholas J White FRS Tropical Medicine University of Oxford United Kingdom
Prof Nicholas PJ Day FMedSci FRCP Tropical Medicine University of Oxford United Kingdom
Prof Adrianus Dondorp Tropical Medicine University of Oxford United Kingdom
Prof Chris V Plowe University of Maryland United States
Dr Rick Fairhurst NIAID NIH United States
Prof François H Nosten Tropical Medicine University of Oxford United Kingdom
Dr Caterina I Fanello Tropical Medicine University of Oxford United Kingdom
Dr Sarah Auburn Menzies Australia
Dr Julian Rayner Wellcome Trust Sanger Institute United Kingdom

Ashley EA, Dhorda M, Fairhurst RM, Amaratunga C, Lim P, Suon S, Sreng S, Anderson JM et al. 2014. Spread of artemisinin resistance in Plasmodium falciparum malaria. N Engl J Med, 371 (5), pp. 411-423. Read abstract | Read more

Artemisinin resistance in Plasmodium falciparum has emerged in Southeast Asia and now poses a threat to the control and elimination of malaria. Mapping the geographic extent of resistance is essential for planning containment and elimination strategies. Hide abstract

Amaratunga C, Witkowski B, Dek D, Try V, Khim N, Miotto O, Ménard D, Fairhurst RM. 2014. Plasmodium falciparum founder populations in western Cambodia have reduced artemisinin sensitivity in vitro. Antimicrob Agents Chemother, 58 (8), pp. 4935-4937. Read abstract | Read more

Reduced Plasmodium falciparum sensitivity to short-course artemisinin (ART) monotherapy manifests as a long parasite clearance half-life. We recently defined three parasite founder populations with long half-lives in Pursat, western Cambodia, where reduced ART sensitivity is prevalent. Using the ring-stage survival assay, we show that these founder populations have reduced ART sensitivity in vitro at the early ring stage of parasite development and that a genetically admixed population contains subsets of parasites with normal or reduced ART sensitivity. Hide abstract

Ariey F, Witkowski B, Amaratunga C, Beghain J, Langlois AC, Khim N, Kim S, Duru V et al. 2014. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria. Nature, 505 (7481), pp. 50-55. Read abstract | Read more

Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain ('K13-propeller') with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread. Hide abstract

Miotto O, Almagro-Garcia J, Manske M, Macinnis B, Campino S, Rockett KA, Amaratunga C, Lim P et al. 2013. Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia. Nat Genet, 45 (6), pp. 648-655. Read abstract | Read more

We describe an analysis of genome variation in 825 P. falciparum samples from Asia and Africa that identifies an unusual pattern of parasite population structure at the epicenter of artemisinin resistance in western Cambodia. Within this relatively small geographic area, we have discovered several distinct but apparently sympatric parasite subpopulations with extremely high levels of genetic differentiation. Of particular interest are three subpopulations, all associated with clinical resistance to artemisinin, which have skewed allele frequency spectra and high levels of haplotype homozygosity, indicative of founder effects and recent population expansion. We provide a catalog of SNPs that show high levels of differentiation in the artemisinin-resistant subpopulations, including codon variants in transporter proteins and DNA mismatch repair proteins. These data provide a population-level genetic framework for investigating the biological origins of artemisinin resistance and for defining molecular markers to assist in its elimination. Hide abstract

Takala-Harrison S, Clark TG, Jacob CG, Cummings MP, Miotto O, Dondorp AM, Fukuda MM, Nosten F et al. 2013. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. Proc Natl Acad Sci U S A, 110 (1), pp. 240-245. Read abstract | Read more

The recent emergence of artemisinin-resistant Plasmodium falciparum malaria in western Cambodia could threaten prospects for malaria elimination. Identification of the genetic basis of resistance would provide tools for molecular surveillance, aiding efforts to contain resistance. Clinical trials of artesunate efficacy were conducted in Bangladesh, in northwestern Thailand near the Myanmar border, and at two sites in western Cambodia. Parasites collected from trial participants were genotyped at 8,079 single nucleotide polymorphisms (SNPs) using a P. falciparum-specific SNP array. Parasite genotypes were examined for signatures of recent positive selection and association with parasite clearance phenotypes to identify regions of the genome associated with artemisinin resistance. Four SNPs on chromosomes 10 (one), 13 (two), and 14 (one) were significantly associated with delayed parasite clearance. The two SNPs on chromosome 13 are in a region of the genome that appears to be under strong recent positive selection in Cambodia. The SNPs on chromosomes 10 and 13 lie in or near genes involved in postreplication repair, a DNA damage-tolerance pathway. Replication and validation studies are needed to refine the location of loci responsible for artemisinin resistance and to understand the mechanism behind it; however, two SNPs on chromosomes 10 and 13 may be useful markers of delayed parasite clearance in surveillance for artemisinin resistance in Southeast Asia. Hide abstract

Williams AR, Douglas AD, Miura K, Illingworth JJ, Choudhary P, Murungi LM, Furze JM, Diouf A et al. 2012. Enhancing blockade of Plasmodium falciparum erythrocyte invasion: assessing combinations of antibodies against PfRH5 and other merozoite antigens. PLoS Pathog, 8 (11), pp. e1002991. Read abstract | Read more

No vaccine has yet proven effective against the blood-stages of Plasmodium falciparum, which cause the symptoms and severe manifestations of malaria. We recently found that PfRH5, a P. falciparum-specific protein expressed in merozoites, is efficiently targeted by broadly-neutralizing, vaccine-induced antibodies. Here we show that antibodies against PfRH5 efficiently inhibit the in vitro growth of short-term-adapted parasite isolates from Cambodia, and that the EC(50) values of antigen-specific antibodies against PfRH5 are lower than those against PfAMA1. Since antibody responses elicited by multiple antigens are speculated to improve the efficacy of blood-stage vaccines, we conducted detailed assessments of parasite growth inhibition by antibodies against PfRH5 in combination with antibodies against seven other merozoite antigens. We found that antibodies against PfRH5 act synergistically with antibodies against certain other merozoite antigens, most notably with antibodies against other erythrocyte-binding antigens such as PfRH4, to inhibit the growth of a homologous P. falciparum clone. A combination of antibodies against PfRH4 and basigin, the erythrocyte receptor for PfRH5, also potently inhibited parasite growth. This methodology provides the first quantitative evidence that polyclonal vaccine-induced antibodies can act synergistically against P. falciparum antigens and should help to guide the rational development of future multi-antigen vaccines. Hide abstract

Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, O'Brien J, Djimde A et al. 2012. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing Nature, 487 (7407), pp. 375-379. Read abstract | Read more

Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance. Here we describe methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P.falciparum genome. © 2012 Macmillan Publishers Limited. All rights reserved. Hide abstract

Auburn S, Campino S, Miotto O, Djimde AA, Zongo I, Manske M, Maslen G, Mangano V et al. 2012. Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data. PLoS One, 7 (2), pp. e32891. Read abstract | Read more

Our understanding of the composition of multi-clonal malarial infections and the epidemiological factors which shape their diversity remain poorly understood. Traditionally within-host diversity has been defined in terms of the multiplicity of infection (MOI) derived by PCR-based genotyping. Massively parallel, single molecule sequencing technologies now enable individual read counts to be derived on genome-wide datasets facilitating the development of new statistical approaches to describe within-host diversity. In this class of measures the F(WS) metric characterizes within-host diversity and its relationship to population level diversity. Utilizing P. falciparum field isolates from patients in West Africa we here explore the relationship between the traditional MOI and F(WS) approaches. F(WS) statistics were derived from read count data at 86,158 SNPs in 64 samples sequenced on the Illumina GA platform. MOI estimates were derived by PCR at the msp-1 and -2 loci. Significant correlations were observed between the two measures, particularly with the msp-1 locus (P = 5.92×10(-5)). The F(WS) metric should be more robust than the PCR-based approach owing to reduced sensitivity to potential locus-specific artifacts. Furthermore the F(WS) metric captures information on a range of parameters which influence out-crossing risk including the number of clones (MOI), their relative proportions and genetic divergence. This approach should provide novel insights into the factors which correlate with, and shape within-host diversity. Hide abstract

Miotto O, Heiny AT, Albrecht R, García-Sastre A, Tan TW, August JT, Brusic V. 2010. Complete-proteome mapping of human influenza A adaptive mutations: implications for human transmissibility of zoonotic strains. PLoS One, 5 (2), pp. e9025. Read abstract | Read more

There is widespread concern that H5N1 avian influenza A viruses will emerge as a pandemic threat, if they become capable of human-to-human (H2H) transmission. Avian strains lack this capability, which suggests that it requires important adaptive mutations. We performed a large-scale comparative analysis of proteins from avian and human strains, to produce a catalogue of mutations associated with H2H transmissibility, and to detect their presence in avian isolates. Hide abstract

Khan AM, Miotto O, Nascimento EJ, Srinivasan KN, Heiny AT, Zhang GL, Marques ET, Tan TW, Brusic V, Salmon J, August JT. 2008. Conservation and variability of dengue virus proteins: implications for vaccine design. PLoS Negl Trop Dis, 2 (8), pp. e272. Read abstract | Read more

Genetic variation and rapid evolution are hallmarks of RNA viruses, the result of high mutation rates in RNA replication and selection of mutants that enhance viral adaptation, including the escape from host immune responses. Variability is uneven across the genome because mutations resulting in a deleterious effect on viral fitness are restricted. RNA viruses are thus marked by protein sites permissive to multiple mutations and sites critical to viral structure-function that are evolutionarily robust and highly conserved. Identification and characterization of the historical dynamics of the conserved sites have relevance to multiple applications, including potential targets for diagnosis, and prophylactic and therapeutic purposes. Hide abstract

Miotto O, Heiny A, Tan TW, August JT, Brusic V. 2008. Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis. BMC Bioinformatics, 9 Suppl 1 (Suppl 1), pp. S18. Read abstract | Read more

The identification of mutations that confer unique properties to a pathogen, such as host range, is of fundamental importance in the fight against disease. This paper describes a novel method for identifying amino acid sites that distinguish specific sets of protein sequences, by comparative analysis of matched alignments. The use of mutual information to identify distinctive residues responsible for functional variants makes this approach highly suitable for analyzing large sets of sequences. To support mutual information analysis, we developed the AVANA software, which utilizes sequence annotations to select sets for comparison, according to user-specified criteria. The method presented was applied to an analysis of influenza A PB2 protein sequences, with the objective of identifying the components of adaptation to human-to-human transmission, and reconstructing the mutation history of these components. Hide abstract

Heiny AT, Miotto O, Srinivasan KN, Khan AM, Zhang GL, Brusic V, Tan TW, August JT. 2007. Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets. PLoS One, 2 (11), pp. e1190. Read abstract | Read more

Influenza A viruses generate an extreme genetic diversity through point mutation and gene segment exchange, resulting in many new strains that emerge from the animal reservoirs, among which was the recent highly pathogenic H5N1 virus. This genetic diversity also endows these viruses with a dynamic adaptability to their habitats, one result being the rapid selection of genomic variants that resist the immune responses of infected hosts. With the possibility of an influenza A pandemic, a critical need is a vaccine that will recognize and protect against any influenza A pathogen. One feasible approach is a vaccine containing conserved immunogenic protein sequences that represent the genotypic diversity of all current and future avian and human influenza viruses as an alternative to current vaccines that address only the known circulating virus strains. Hide abstract

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