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Keita AK, Mbaye A, Soumah AK, Kadio KJJO, Diallo H, Gnimadi TAC, Koivogui JB, Povogui MK, Monemou JL, Traore B, Vidal N, Guichet E, Ayouba A, Delaporte E, Peeters M, Toure A, Keita AK. Use of strips of rapid diagnostic tests as a source of ribonucleic acid for genomic surveillance of viruses: an example of SARS-CoV-2. Virol J 2024; 21:171. [PMID: 39090721 PMCID: PMC11295317 DOI: 10.1186/s12985-024-02442-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND This study aimed to demonstrate that the genomic material of SARS-CoV-2 can be isolated from strips of COVID-19 rapid diagnostic test cassettes. METHOD It was a prospective cross-sectional study involving patients admitted to treatment centers and sampling sites in the city of Conakry, Guinea. A total of 121 patients were double sampled, and 9 more patients were tested only for RDT. PCR was conducted according to the protocol of the RunMei kit. Sequencing was performed by using the illumina COVIDSeq protocol. Nine COVID-19 RDTs without nasopharyngeal swabs were in addition tested. RESULT Among the 130 COVID-19 RDTs, forty-seven were macroscopically positive, whereas seventy-two were positive according to PCR using RDT strip, while among the 121 VTM swabs, sixty-four were positive. Among eighty-three negative COVID-19 RDTs, twenty-seven were positive by PCR using RDT strip with a geometric mean Ct value of 32.49 cycles. Compared to those of PCR using VTM, the sensitivity and specificity of PCR using RDT strip were estimated to be 100% and 85.96%, respectively, with 93.39% test accuracy. Among the fifteen COVID-19 RDT extracts eligible for sequencing, eleven had sequences identical to those obtained via the standard method, with coverage between 75 and 99.6%. CONCLUSION These results show that COVID-19 RDTs can be used as biological material for the genomic surveillance of SARS-CoV-2.
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Affiliation(s)
- Alpha Kabiné Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Aminata Mbaye
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea.
| | - Abdoul Karim Soumah
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Kadio Jean Jacques Olivier Kadio
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Haby Diallo
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Thibaut Armel Chérif Gnimadi
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Joel Balla Koivogui
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Moriba Kowa Povogui
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Jean Louis Monemou
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Baba Traore
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Nicole Vidal
- Institut de Recherche pour le Développement (IRD), INSERM, TransVIHMI, University of Montpellier, Montpellier, France
| | - Emilande Guichet
- Institut de Recherche pour le Développement (IRD), INSERM, TransVIHMI, University of Montpellier, Montpellier, France
| | - Ahidjo Ayouba
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
- Institut de Recherche pour le Développement (IRD), INSERM, TransVIHMI, University of Montpellier, Montpellier, France
| | - Eric Delaporte
- Institut de Recherche pour le Développement (IRD), INSERM, TransVIHMI, University of Montpellier, Montpellier, France
| | - Martine Peeters
- Institut de Recherche pour le Développement (IRD), INSERM, TransVIHMI, University of Montpellier, Montpellier, France
| | - Abdoulaye Toure
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Alpha Kabinet Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
- Institut de Recherche pour le Développement (IRD), INSERM, TransVIHMI, University of Montpellier, Montpellier, France
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El Hadji Ibrahima N, Diatta G, Adama Zan D, Bassene H, Sokhna C, Parola P. Quantitative Polymerase Chain Reaction from Malaria Rapid Diagnostic Tests to Detect Borrelia crocidurae, the Agent of Tick-Borne Relapsing Fever, in Febrile Patients in Senegal. Am J Trop Med Hyg 2023; 108:968-976. [PMID: 36913922 PMCID: PMC10160891 DOI: 10.4269/ajtmh.22-0342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/29/2022] [Indexed: 03/14/2023] Open
Abstract
In endemic malaria areas, Plasmodium is currently diagnosed mainly through the use of rapid diagnostic tests (RDTs). However, in Senegal, many causes of fever remain unknown. Tick-borne relapsing fever, an often-neglected public health problem, is the main cause of consultation for acute febrile illness after malaria and flu in rural areas. Our objective was to test the feasibility of extracting and amplifying DNA fragments by quantitative polymerase chain reaction (qPCR) from malaria-negative RDTs for Plasmodium falciparum (malaria Neg RDTs P.f) to detect Borrelia spp. and other bacteria. Between January and December 2019, malaria Neg RDTs P.f were collected on a quarterly basis in 12 health facilities in four regions of Senegal. The DNA extracted from the malaria Neg RDTs P.f was tested using qPCR and the results were confirmed by standard PCR and sequencing. Only Borrelia crocidurae DNA was detected in 7.22% (159/2,202) of RDTs. The prevalence of B. crocidurae DNA was higher in July (16.47%, 43/261) and August (11.21%, 50/446). The annual prevalence was 9.2% (47/512) and 5.0% (12/241) in Ngayokhem and Nema-Nding, respectively, health facilities in the Fatick region. Our study confirms that B. crocidurae infection is a frequent cause of fever in Senegal, with a high prevalence of cases in health facilities in the regions of Fatick and Kaffrine. Malaria Neg RDTs P.f are potentially a good source of pathogen sampling for the molecular identification of other causes of fever of unknown origin, even in the most remote areas.
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Affiliation(s)
- Ndiaye El Hadji Ibrahima
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), APHM, SSA, Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France
- VITROME, IRD UMR 257, Campus International IRD-UCAD Hann, Dakar, Sénégal
| | - Georges Diatta
- VITROME, IRD UMR 257, Campus International IRD-UCAD Hann, Dakar, Sénégal
| | - Diarra Adama Zan
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), APHM, SSA, Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France
| | - Hubert Bassene
- VITROME, IRD UMR 257, Campus International IRD-UCAD Hann, Dakar, Sénégal
| | - Cheikh Sokhna
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France
- VITROME, IRD UMR 257, Campus International IRD-UCAD Hann, Dakar, Sénégal
| | - Philippe Parola
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), APHM, SSA, Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France
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Mauhay JD, Saito N, Kimitsuki K, Mananggit MR, Cruz JL, Lagayan MG, Garcia AM, Lacanilao PM, Yamada K, Saito-Obata M, Manalo DL, Demetria CS, Quiambao BP, Nishizono A. Molecular Analysis of Rabies Virus Using RNA Extracted from Used Lateral Flow Devices. J Clin Microbiol 2023; 61:e0154322. [PMID: 36840574 PMCID: PMC10035306 DOI: 10.1128/jcm.01543-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Molecular analysis of rabies virus can provide accurate diagnosis and information on its genetic diversity. The transportation of rabies brain samples from remote areas to a central laboratory is challenging owing to biohazard risks and decomposability. We investigated the utility of used lateral flow devices (LFDs) for subsequent molecular analysis and assessed the necessary storage temperatures. Using RNA extracted from used LFD strips, we performed conventional reverse transcription-PCR (RT-PCR) using an LN34 primer set to amplify short fragments (165 bp) for rabies virus detection and the P1-304 primer set to amplify long fragments of the entire N gene amplicon (1,506 bp) for phylogenetic analysis. Among 71 used LFDs stored in a refrigerator and 64 used LFDs stored at room temperature, the LN34 assay showed high sensitivities (96.2% and 100%, respectively) for the diagnosis of rabies, regardless of the storage temperature. A significant reduction in the sensitivity of rabies diagnosis was observed when using the P1-304 primer set for used LFDs stored at room temperature compared to those stored at refrigeration temperature (20.9% versus 100%; P < 0.05). Subsequent sequencing and phylogenetic analysis were successfully performed using the amplicons generated by the P1-304 RT-PCR assays. Used LFDs are thus promising resources for rabies virus RNA detection and sequence analysis. Virus detection via RT-PCR, amplifying a short fragment, was possible regardless of the storage temperature of the used LFDs. However, refrigerated storage is recommended for RT-PCR amplification of long fragments for phylogenetic analysis.
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Affiliation(s)
- Jaira D Mauhay
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Nobuo Saito
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Oita, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Nagasaki, Japan
| | - Kazunori Kimitsuki
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Milagros R Mananggit
- Regional Animal Disease Diagnostic Laboratory, Department of Agriculture Field Office III, San Fernando, Pampanga, Philippines
| | - Jeffrey L Cruz
- Department of Agriculture, Bureau of Animal Industry, Quezon, National Capital Region, Philippines
| | - Maria G Lagayan
- Department of Agriculture, Bureau of Animal Industry, Quezon, National Capital Region, Philippines
| | - Alyssa M Garcia
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Patricia M Lacanilao
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Kentaro Yamada
- Laboratory of Veterinary Public Health, Department of Veterinary Medical Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | | | - Daria L Manalo
- Research Institute for Tropical Medicine, Muntinlupa, National Capital Region, Philippines
| | - Catalino S Demetria
- Research Institute for Tropical Medicine, Muntinlupa, National Capital Region, Philippines
| | - Beatriz P Quiambao
- Research Institute for Tropical Medicine, Muntinlupa, National Capital Region, Philippines
| | - Akira Nishizono
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Oita, Japan
- Research Center for Global and Local Infectious Diseases, Faculty of Medicine, Oita University, Yufu, Oita, Japan
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Andrianaranjaka VHI, Ravaoarisoa E, Rakotomanga TA, Ralinoro F, Rakoto DAD, Randrianarivo RH, Jeannoda V, Ratsimbasoa A. DNA recovery from used malaria RDT to detect Plasmodium species and to assess Plasmodium falciparum genetic diversity: a pilot study in Madagascar. Malar J 2022; 21:227. [PMID: 35883089 PMCID: PMC9327223 DOI: 10.1186/s12936-022-04246-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Rapid diagnostic tests (RDT) are widely used for malaria diagnosis in Madagascar, where Plasmodium falciparum is the predominant species. Molecular diagnosis is essential for malaria surveillance, but requires additional blood samples for DNA extraction. Used RDTs is an attractive alternative that can be used as a source of DNA. Plasmodium falciparum genetic diversity and multiplicity of infection, usually determined by the genotyping of polymorphic regions of merozoite surface proteins 1 and 2 genes (msp1, msp2), and the repeated region RII of the glutamate-rich protein gene (glurp) have been associated with malaria transmission levels and subsequently with the impact of the deployed control strategies. Thus, the study aims to use RDT as DNA source to detect Plasmodium species, to characterize Plasmodium falciparum genetic diversity and determine the multiplicity of infection. Methods A pilot study was conducted in two sites with different epidemiological patterns: Ankazomborona (low transmission area) and Matanga (high transmission area). On May 2018, used RDT (SD BIOLINE Malaria Ag P.f/Pan, 05FK63) were collected as DNA source. Plasmodium DNA was extracted by simple elution with nuclease free water. Nested-PCR were performed to confirm Plasmodium species and to analyse P. falciparum msp1, msp2 and glurp genes polymorphisms. Results Amongst the 170 obtained samples (N = 74 from Ankazomborona and N = 96 from Matanga), Plasmodium positivity rate was 23.5% (40/170) [95% CI 17.5–30.8%] by nested-PCR with 92.2% (37/40) positive to P. falciparum, 5% (2/40) to Plasmodium vivax and 2.5% (1/40) to P. falciparum/P. vivax mixed infection. Results showed high polymorphisms in P. falciparum msp1, msp2 and glurp genes. Multiple infection rate was 28.6% [95% CI 12.2–52.3%]. The mean of MOI was 1.79 ± 0.74. Conclusion This pilot study highlighted that malaria diagnosis and molecular analysis are possible by using used malaria RDT. A large-scale study needs to be conducted to assess more comprehensively malaria parasites transmission levels and provide new data for guiding the implementation of local strategies for malaria control and elimination. Trial registration Retrospectively registered
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Affiliation(s)
- Voahangy Hanitriniaina I Andrianaranjaka
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar. .,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar.
| | - Elisabeth Ravaoarisoa
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Tovonahary A Rakotomanga
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Fanomezantsoa Ralinoro
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Danielle A Doll Rakoto
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Ranjàna H Randrianarivo
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Victor Jeannoda
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Arsène Ratsimbasoa
- Faculté de Médecine, Université de Fianarantsoa, Fianarantsoa, Madagascar.,Centre National d'Application de Recherche Pharmaceutique, Antananarivo, Madagascar
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O'Flaherty K, Oo WH, Zaloumis SG, Cutts JC, Aung KZ, Thein MM, Drew DR, Razook Z, Barry AE, Parischa N, Zaw NN, Thu HK, Thi A, Htay WYM, Soe AP, Simpson JA, Beeson JG, Agius PA, Fowkes FJI. Community-based molecular and serological surveillance of subclinical malaria in Myanmar. BMC Med 2021; 19:121. [PMID: 34044836 PMCID: PMC8161608 DOI: 10.1186/s12916-021-01993-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/27/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND In the Greater Mekong Subregion (GMS), current malaria surveillance strategies rely on a network of village health volunteers (VHVs) reporting the results of rapid diagnostic tests (RDTs), known to miss many asymptomatic infections. Integration of more sensitive diagnostic molecular and serological measures into the VHV network may improve surveillance of residual malaria transmission in hard-to-reach areas in the region and inform targeted interventions and elimination responses. However, data on residual malaria transmission that would be captured by these measures in the VHV-led testing and treatment surveillance network in the GMS is unknown. METHODS A total of 114 VHVs were trained to collect dried blood spots from villagers undergoing routine RDTs as part of VHV-led active and passive case detection from April 2015 to June 2016. Samples were subjected to molecular testing (quantitative polymerase chain reaction [qPCR]) to determine Plasmodium falciparum and P. vivax infection and serological testing (against P. falciparum and P. vivax antigens) to determine exposure to P. falciparum and P. vivax. RESULTS Over 15 months, 114 VHVs performed 32,194 RDTs and collected samples for molecular (n = 13,157) and serological (n = 14,128) testing. The prevalence of molecular-detectable P. falciparum and P. vivax infection was 3.2% compared to the 0.16% prevalence of Plasmodium spp. by RDT, highlighting the large burden of infections undetected by standard surveillance. Peaks in anti-P. falciparum, but not P. vivax, merozoite IgG seroprevalence coincided with seasonal P. falciparum transmission peaks, even in those with no molecularly detectable parasites. At the individual level, antibody seropositivity was associated with reduced odds of contemporaneous P. falciparum (OR for PfCSP 0.51 [95%CI 0.35, 0.76], p = 0.001, PfAMA1 0.70 [95%CI 0.52, 0.93], p = 0.01, and PfMSP2 0.81 [95%CI 0.61, 1.08], p = 0.15), but not P. vivax infection (OR PvAMA1 1.02 [95%CI 0.73, 1.43], p = 0.89) indicating a potential role of immunity in protection against molecular-detectable P. falciparum parasitaemia. CONCLUSIONS We demonstrated that integration and implementation of sample collection for molecular and serological surveillance into networks of VHV servicing hard-to-reach populations in the GMS is feasible, can capture significant levels of ongoing undetected seasonal malaria transmission and has the potential to supplement current routine RDT testing. Improving malaria surveillance by advancing the integration of molecular and serological techniques, through centralised testing approaches or novel point-of-contact tests, will advance progress, and tracking, towards malaria elimination goals in the GMS.
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Affiliation(s)
- Katherine O'Flaherty
- Burnet Institute for Medical Research and Public Health, Melbourne, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Win Han Oo
- Burnet Institute Myanmar, Yangon, Myanmar
| | - Sophie G Zaloumis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Julia C Cutts
- Burnet Institute for Medical Research and Public Health, Melbourne, Australia.,Department of Medicine, University of Melbourne, Melbourne, Australia
| | | | | | - Damien R Drew
- Burnet Institute for Medical Research and Public Health, Melbourne, Australia
| | - Zahra Razook
- School of Medicine, Deakin University, Geelong, Australia
| | - Alyssa E Barry
- Burnet Institute for Medical Research and Public Health, Melbourne, Australia.,Department of Medicine, University of Melbourne, Melbourne, Australia.,School of Medicine, Deakin University, Geelong, Australia
| | - Naanki Parischa
- Burnet Institute for Medical Research and Public Health, Melbourne, Australia
| | | | | | - Aung Thi
- Department of Public Health, Myanmar Ministry of Health, Nay Pyi Taw, Myanmar
| | | | | | - Julie A Simpson
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - James G Beeson
- Burnet Institute for Medical Research and Public Health, Melbourne, Australia.,Department of Medicine, University of Melbourne, Melbourne, Australia.,Department of Microbiology and Central Clinical School, Monash University, Melbourne, Australia
| | - Paul A Agius
- Burnet Institute for Medical Research and Public Health, Melbourne, Australia.,Department of Epidemiology and Preventative Medicine, Monash University, Melbourne, Australia.,Judith Lumley Centre, La Trobe University, Melbourne, Australia
| | - Freya J I Fowkes
- Burnet Institute for Medical Research and Public Health, Melbourne, Australia. .,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia. .,Department of Epidemiology and Preventative Medicine, Monash University, Melbourne, Australia. .,Department of Infectious Diseases, Monash University, Melbourne, Australia.
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6
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Liu S, Huckaby AC, Brown AC, Moore CC, Burbulis I, McConnell MJ, Güler JL. Single-cell sequencing of the small and AT-skewed genome of malaria parasites. Genome Med 2021; 13:75. [PMID: 33947449 PMCID: PMC8094492 DOI: 10.1186/s13073-021-00889-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/17/2021] [Indexed: 12/23/2022] Open
Abstract
Single-cell genomics is a rapidly advancing field; however, most techniques are designed for mammalian cells. We present a single-cell sequencing pipeline for an intracellular parasite, Plasmodium falciparum, with a small genome of extreme base content. Through optimization of a quasi-linear amplification method, we target the parasite genome over contaminants and generate coverage levels allowing detection of minor genetic variants. This work, as well as efforts that build on these findings, will enable detection of parasite heterogeneity contributing to P. falciparum adaptation. Furthermore, this study provides a framework for optimizing single-cell amplification and variant analysis in challenging genomes.
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Affiliation(s)
- Shiwei Liu
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Adam C Huckaby
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Audrey C Brown
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Christopher C Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Ian Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
- Current address: Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Jennifer L Güler
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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McDaniels JM, Huckaby AC, Carter SA, Lingeman S, Francis A, Congdon M, Santos W, Rathod PK, Guler JL. Extrachromosomal DNA amplicons in antimalarial-resistant Plasmodium falciparum. Mol Microbiol 2021; 115:574-590. [PMID: 33053232 PMCID: PMC8246734 DOI: 10.1111/mmi.14624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 12/29/2022]
Abstract
Extrachromosomal (ec) DNAs are genetic elements that exist separately from the genome. Since ecDNA can carry beneficial genes, they are a powerful adaptive mechanism in cancers and many pathogens. For the first time, we report ecDNA contributing to antimalarial resistance in Plasmodium falciparum, the most virulent human malaria parasite. Using pulse field gel electrophoresis combined with PCR-based copy number analysis, we detected two ecDNA elements that differ in migration and structure. Entrapment in the electrophoresis well and low susceptibility to exonucleases revealed that the biologically relevant ecDNA element is large and complex in structure. Using deep sequencing, we show that ecDNA originates from the chromosome and expansion of an ecDNA-specific sequence may improve its segregation or expression. We speculate that ecDNA is maintained using established mechanisms due to shared characteristics with the mitochondrial genome. Implications of ecDNA discovery in this organism are wide-reaching due to the potential for new strategies to target resistance development.
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Affiliation(s)
| | - Adam C. Huckaby
- Department of BiologyUniversity of VirginiaCharlottesvilleVAUSA
| | | | | | - Audrey Francis
- Department of BiologyUniversity of VirginiaCharlottesvilleVAUSA
| | | | | | | | - Jennifer L. Guler
- Department of BiologyUniversity of VirginiaCharlottesvilleVAUSA
- Division of Infectious Diseases and International HealthDepartment of MedicineUniversity of VirginiaCharlottesvilleVAUSA
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