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Bouska O, Koudelakova V, Gurska S, Kubanova K, Slavkovsky R, Jaworek H, Vrbkova J, Dzubak P, Hajduch M. Pooling of samples to optimise SARS-CoV-2 detection in nasopharyngeal swabs and gargle lavage self-samples for covid-19 diagnostics and surveillance. Infect Dis (Lond) 2024; 56:531-542. [PMID: 38549542 DOI: 10.1080/23744235.2024.2333438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/16/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Testing of pooled samples is an effective strategy for increasing testing capacity while saving resources and time. This study aimed to validate pooled testing and gather real-life data on its use for Covid-19 surveillance with a gargle lavage (GL) self-sampling strategy. METHODS Two-stage pooled testing with pools of 6 and 12 samples was used for preventive testing of an asymptomatic population and Covid-19 surveillance in Czech schools. Both GL and nasopharyngeal swabs were used for sampling. RESULTS In total, 61,111 samples were tested. The use of pooled testing for large-scale Covid-19 surveillance reduced consumable costs by almost 75% and increased testing capacity up to 3.8-fold compared to standard methods. RT-PCR experiments revealed a minimal loss of sensitivity (0-2.2%) when using pooled samples, enabling the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes with Ct values >35. The minor loss of sensitivity was counterbalanced by a significantly increased throughput and the ability to substantially increase testing frequencies. CONCLUSIONS Pooled testing is considerably more cost-effective and less time-consuming than standard testing for large-scale Covid-19 surveillance even when the prevalence of SARS-CoV-2 is fluctuating. Gargle lavage self-sampling is a non-invasive technique suitable for sample collection without a healthcare worker's assistance.
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Affiliation(s)
- Ondrej Bouska
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Vladimira Koudelakova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- Laboratory of Experimental Medicine, University Hospital Olomouc, Olomouc, Czech Republic
| | - Sona Gurska
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Katerina Kubanova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Rastislav Slavkovsky
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Hana Jaworek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- Laboratory of Experimental Medicine, University Hospital Olomouc, Olomouc, Czech Republic
| | - Jana Vrbkova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Petr Dzubak
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- Laboratory of Experimental Medicine, University Hospital Olomouc, Olomouc, Czech Republic
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Akafity G, Kumi N, Ashong J. Diagnosis and management of malaria in the intensive care unit. JOURNAL OF INTENSIVE MEDICINE 2024; 4:3-15. [PMID: 38263976 PMCID: PMC10800773 DOI: 10.1016/j.jointm.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/17/2023] [Accepted: 09/02/2023] [Indexed: 01/25/2024]
Abstract
Malaria is responsible for approximately three-quarters of a million deaths in humans globally each year. Most of the morbidity and mortality reported are from Sub-Saharan Africa and Asia, where the disease is endemic. In non-endemic areas, malaria is the most common cause of imported infection and is associated with significant mortality despite recent advancements and investments in elimination programs. Severe malaria often requires intensive care unit admission and can be complicated by cerebral malaria, respiratory distress, acute kidney injury, bleeding complications, and co-infection. Intensive care management includes prompt diagnosis and early initiation of effective antimalarial therapy, recognition of complications, and appropriate supportive care. However, the lack of diagnostic capacities due to limited advances in equipment, personnel, and infrastructure presents a challenge to the effective diagnosis and management of malaria. This article reviews the clinical classification, diagnosis, and management of malaria as relevant to critical care clinicians, highlighting the role of diagnostic capacity, treatment options, and supportive care.
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Affiliation(s)
- George Akafity
- Department of Research, Monitoring, and Evaluation, Cape Coast Teaching Hospital, Cape Coast, Ghana
| | - Nicholas Kumi
- Intensive Care Unit, Department of Critical Care and Anesthesia, Cape Coast Teaching Hospital, Cape Coast, Ghana
| | - Joyce Ashong
- Department of Paediatrics and Child Health, Cape Coast Teaching Hospital, Cape Coast, Ghana
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Effectiveness of sample pooling strategies for diagnosis of SARS-CoV-2: Specimen pooling vs. RNA elutes pooling. Indian J Med Microbiol 2023; 42:34-38. [PMID: 36967213 PMCID: PMC9870240 DOI: 10.1016/j.ijmmb.2022.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/13/2022] [Accepted: 12/31/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE The pandemic of SARS-CoV-2 or COVID-19 has hugely created an economic imbalance worldwide. With the exponential increase in the number of cases and to keep in check on the community transmission, there is high demand and acute shortage of diagnostic kits. The pooled-sample strategy turns out to be the promising strategy intended to determine the optimal testing for specimens with limited resources and without losing the test sensitivity and specificity. The study was performed with standard molecular biology graded lab equipment, FDA-approved COVID-19 RNA extraction, and SARS-CoV-2 tests kits. MATERIALS AND METHODS The study aims to comparatively analyze the pooling strategy of the naso-oropharyngeal specimen sample and RNA extracted from the same patient samples in the pool of 3,5, and 8 with no significant loss in test usability. Another primary focus of the study was detection of low or borderline SARS-CoV-2 positives in the pooling strategy. A total of 300 samples (240 positives and 60 negatives) were tested for 3, 5, and 8 pools of specimen samples and RNA elutes. RESULTS The comparative analysis determined the sensitivity for three and five pool strategy to be above 98% and eight pool strategy to be 100%. CONCLUSION The RNA elutes pooling strategy concordance rate is better than that of specimen pooling with 100% specificity. Thus, in the substantial crisis of resources with the global pandemic, pooling approaches for SARS-CoV-2 can be practical in a low prevalence rate of 5%.
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Shah MP, Chebore W, Lyles RH, Otieno K, Zhou Z, Plucinski M, Waller LA, Odongo W, Lindblade KA, Kariuki S, Samuels AM, Desai M, Mitchell RM, Shi YP. Novel application of one-step pooled molecular testing and maximum likelihood approaches to estimate the prevalence of malaria parasitaemia among rapid diagnostic test negative samples in western Kenya. Malar J 2022; 21:319. [PMID: 36336700 PMCID: PMC9638440 DOI: 10.1186/s12936-022-04323-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/07/2022] [Indexed: 11/08/2022] Open
Abstract
Abstract
Background
Detection of malaria parasitaemia in samples that are negative by rapid diagnostic tests (RDTs) requires resource-intensive molecular tools. While pooled testing using a two-step strategy provides a cost-saving alternative to the gold standard of individual sample testing, statistical adjustments are needed to improve accuracy of prevalence estimates for a single step pooled testing strategy.
Methods
A random sample of 4670 malaria RDT negative dried blood spot samples were selected from a mass testing and treatment trial in Asembo, Gem, and Karemo, western Kenya. Samples were tested for malaria individually and in pools of five, 934 pools, by one-step quantitative polymerase chain reaction (qPCR). Maximum likelihood approaches were used to estimate subpatent parasitaemia (RDT-negative, qPCR-positive) prevalence by pooling, assuming poolwise sensitivity and specificity was either 100% (strategy A) or imperfect (strategy B). To improve and illustrate the practicality of this estimation approach, a validation study was constructed from pools allocated at random into main (734 pools) and validation (200 pools) subsets. Prevalence was estimated using strategies A and B and an inverse-variance weighted estimator and estimates were weighted to account for differential sampling rates by area.
Results
The prevalence of subpatent parasitaemia was 14.5% (95% CI 13.6–15.3%) by individual qPCR, 9.5% (95% CI (8.5–10.5%) by strategy A, and 13.9% (95% CI 12.6–15.2%) by strategy B. In the validation study, the prevalence by individual qPCR was 13.5% (95% CI 12.4–14.7%) in the main subset, 8.9% (95% CI 7.9–9.9%) by strategy A, 11.4% (95% CI 9.9–12.9%) by strategy B, and 12.8% (95% CI 11.2–14.3%) using inverse-variance weighted estimator from poolwise validation. Pooling, including a 20% validation subset, reduced costs by 52% compared to individual testing.
Conclusions
Compared to individual testing, a one-step pooled testing strategy with an internal validation subset can provide accurate prevalence estimates of PCR-positivity among RDT-negatives at a lower cost.
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Jain S, Bhowmick A, Pandey AK. A rapid One-Pot RNA isolation method for simplified clinical detection of SARS-COV-2 infection in India. Front Cell Infect Microbiol 2022. [DOI: 10.3389/fcimb.2022.962057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BackgroundWith the rapid increase in COVID-19 cases and the discovery of new viral variants within India over multiple waves, the expensive reagents and time-consuming sample pretreatment required for qPCR analysis have led to slower detection of the disease. The vast Indian population demands an inexpensive and competent sample preparation strategy for rapid detection of the disease facilitating early and efficient containment of the disease.MethodsIn this study, we have surveyed the spread of COVID-19 infection over Faridabad, Haryana, India for 6 months. We also devised a simple single-step method for total RNA extraction using a single tube and compared its efficacy with the commercially available RNA isolation kits.FindingsOur findings suggest that determining Ct values for samples subjected to the One Pot RNA extraction method was as efficient as the commercially available kits but delivers a subtle advantage in a way, by minimizing the cost, labor and sample preparation time.ConclusionThis novel crude RNA extraction method is stable and capable of operating in developing countries like India for low resource settings, without the use of expensive reagents and instruments. Additionally, this method can be further adapted to pooling samples strategies owing to its high sensitivity.
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Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond. PLoS Comput Biol 2022; 18:e1010629. [PMID: 36279287 PMCID: PMC9632879 DOI: 10.1371/journal.pcbi.1010629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/03/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
The rapid spread of SARS-CoV-2 has placed a significant burden on public health systems to provide swift and accurate diagnostic testing highlighting the critical need for innovative testing approaches for future pandemics. In this study, we present a novel sample pooling procedure based on compressed sensing theory to accurately identify virally infected patients at high prevalence rates utilizing an innovative viral RNA extraction process to minimize sample dilution. At prevalence rates ranging from 0-14.3%, the number of tests required to identify the infection status of all patients was reduced by 69.26% as compared to conventional testing in primary human SARS-CoV-2 nasopharyngeal swabs and a coronavirus model system. Our method provided quantification of individual sample viral load within a pool as well as a binary positive-negative result. Additionally, our modified pooling and RNA extraction process minimized sample dilution which remained constant as pool sizes increased. Compressed sensing can be adapted to a wide variety of diagnostic testing applications to increase throughput for routine laboratory testing as well as a means to increase testing capacity to combat future pandemics.
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Molecular assays for determining sulphadoxine-pyrimethamine drug resistance in India: a systematic review. Parasitol Res 2022; 121:2765-2774. [PMID: 35980472 DOI: 10.1007/s00436-022-07623-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/08/2022] [Indexed: 10/15/2022]
Abstract
A plethora of studies analyse the molecular markers of drug resistance and hence help in guiding the evidence-based malaria treatment policies in India. For reporting mutations, a number of techniques including DNA sequencing, restriction-fragment length polymorphism and mutation-specific polymerase chain reaction have been employed across numerous studies, including variations in the methodology used. However, there is no sufficient data from India comparing these methods as well as report the prevalence of polymorphisms in SP drug resistance molecular markers independently using such methods. Therefore, all data from Indian studies available for molecular marker studies of Plasmodium falciparum drug resistance to sulphadoxine-pyrimethamine was gathered, and a systematic review was performed. This systematic review identifies the molecular methods in use in India and compares each method for detecting sulphadoxine-pyrimethamine drug resistance marker. To delay the spread of drug-resistant parasite strains, a simplified and standardized molecular method is much needed which can be obtained by analysing the performance of each method in use and answering the necessity of newer methodological approaches.
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Han KT, Han ZY, Zainabadi K. Developing Molecular Surveillance Capacity for Asymptomatic and Drug-Resistant Malaria in a Resource-Limited Setting-Experiences and Lessons Learned. Am J Trop Med Hyg 2022; 107:222-230. [PMID: 35895423 PMCID: PMC9393433 DOI: 10.4269/ajtmh.21-0543] [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: 05/19/2021] [Accepted: 10/15/2021] [Indexed: 08/03/2023] Open
Abstract
The COVID-19 pandemic has highlighted the important role molecular surveillance plays in public health. Such capacity however is either weak or nonexistent in many low-income countries. This article outlines a 2-year effort to establish two high-throughput molecular surveillance laboratories in Myanmar for tracking asymptomatic and drug resistant Plasmodium falciparum malaria. The lessons learned from this endeavor may prove useful for others seeking to establish similar molecular surveillance capacity in other resource-limited settings.
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Affiliation(s)
- Kay Thwe Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Zay Yar Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Kayvan Zainabadi
- Center for Global Health, Weill Cornell Medicine, New York, New York
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Lin H, Zhao S, Liu Y, Shao L, Ye Y, Jiang N, Yang K. Rapid Visual Detection of Plasmodium Using Recombinase-Aided Amplification With Lateral Flow Dipstick Assay. Front Cell Infect Microbiol 2022; 12:922146. [PMID: 35811679 PMCID: PMC9263184 DOI: 10.3389/fcimb.2022.922146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/24/2022] [Indexed: 12/14/2022] Open
Abstract
Background Malaria is a global public health problem. China has had no case of indigenous malaria since 2016. However, imported cases of malaria remain an issue among travelers, overseas workers, and foreign traders. Although these cases are always asymptomatic, if they donate blood, there is a great risk of transfusion transmitted-malaria (TTM). Therefore, blood banks need a rapid screening tool to detect Plasmodium species. Methods We designed an assay using recombinase-aided amplification (RAA) and a lateral-flow dipstick (LFD) (RAA-LFD) to detect the 18S ribosomal RNA gene of Plasmodium species. Sensitivity was evaluated using a recombinant plasmid and Plasmodium genomic DNA. Specificity was evaluated using DNA extracted from the blood of patients with malaria or other infectious parasites. For clinical assessment, blood samples from patients with malaria and blood donors were evaluated. Results The RAA-LFD assay was performed in an incubator block at 37°C for 15 min, and the amplicons were visible to the naked eye on the flow dipsticks within 3 min. The sensitivity was 1 copy/μL of recombinant plasmid. For genomic DNA from whole blood of malaria patients infected with P. falciparum, P. vivax, P. ovale, and P. malariae, the sensitivity was 0.1 pg/μL, 10 pg/μL, 10-100 pg/μL, and 100pg/μL, respectively. The sensitivity of this assay was 100pg/μL. No cross-reaction with other transfusion-transmissible parasites was detected. Conclusions The results demonstrated that this RAA-LFD assay was suitable for reliable field detection of Plasmodium species in low-resource settings with limited laboratory capabilities.
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Affiliation(s)
- Hong Lin
- Jiangsu Province Blood Center, Nanjing, China
- *Correspondence: Hong Lin, ; Kun Yang,
| | - Song Zhao
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yanhong Liu
- Jiangsu Qitian Gene Technology Co., Ltd., Wuxi, China
| | - Lei Shao
- Jiangsu Province Blood Center, Nanjing, China
| | - Yuying Ye
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | | | - Kun Yang
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
- *Correspondence: Hong Lin, ; Kun Yang,
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Phan T, Tran NYK, Gottlieb T, Siarakas S, McKew G. Evaluation of the influenza and respiratory syncytial virus (RSV) targets in the AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay: sample pooling increases testing throughput. Pathology 2022; 54:466-471. [PMID: 35461715 PMCID: PMC9021007 DOI: 10.1016/j.pathol.2022.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/09/2022] [Accepted: 02/22/2022] [Indexed: 02/06/2023]
Abstract
During the COVID-19 pandemic, sample pooling has proven an effective strategy to overcome the limitations of reagent shortages and expand laboratory testing capacity. The inclusion of influenza and respiratory syncytial virus (RSV) in a multiplex tandem PCR platform with SARS-CoV-2 provides useful diagnostic and infection control information. This study aimed to evaluate the performance of the influenza and RSV targets in the AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay, including the effect of pooling samples on target detection. RSV target detection in clinical samples was compared to the Cepheid Xpert Xpress Flu/RSV assay as a reference standard. Samples were then tested in pools of four and detection rates were compared. Owing to the unavailability of clinical samples for influenza, only the effect of sample pooling on simulated samples was evaluated for these targets. RSV was detected in neat clinical samples with a positive percent agreement (PPA) of 100% and negative percent agreement (NPA) of 99.5% compared to the reference standard, demonstrating 99.7% agreement. This study demonstrates that sample pooling by four increases the average Ct value by 2.24, 2.29, 2.20 and 1.91 cycles for the target's influenza A, influenza A typing, influenza B and RSV, respectively. The commercial AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay was able to detect influenza and RSV at an intermediate concentration within the limit of detection of the assay. Further studies to explore the applicability of sample pooling at the lower limit of detection of the assay is needed. Nevertheless, sample pooling has shown to be a viable strategy to increase testing throughput and reduce reagent usage. In addition, the multiplexed platform targeting various respiratory viruses assists with public health and infection control responses, clinical care, and patient management.
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Affiliation(s)
- Thuy Phan
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia
| | - Ngoc Yen Kim Tran
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia.
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Concord, NSW, Australia
| | - Steven Siarakas
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia
| | - Genevieve McKew
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Concord, NSW, Australia
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Edgel KA, Canavati S, Le HT, Tran TH, Van Nguyen K, Nguyen TV, Nguyen NT, Tran HM, Ngo TD, Tran DT, Nguyen BTH, Tran LK, Nguyen TM, Whedbee RJ, Milgotina EI, Martin NJ. Understanding the epidemiology, clinical characteristics, knowledge and barriers to treatment and prevention of malaria among returning international laborers in northern Vietnam: a mixed-methods study. BMC Infect Dis 2022; 22:460. [PMID: 35562690 PMCID: PMC9102356 DOI: 10.1186/s12879-022-07322-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With the decline in local malaria transmission in Vietnam as a result of the National Malaria Control Program (NMCP) elimination activities, a greater focus on the importation and potential reintroduction of transmission are essential to support malaria elimination objectives. METHODS We conducted a multi-method assessment of the demographics, epidemiology, and clinical characteristics of imported malaria among international laborers returning from African or Southeast Asian countries to Vietnam. Firstly, we conducted a retrospective review of hospital records of patients from January 2014 to December 2016. Secondly, we conducted a mixed-methods prospective study for malaria patients admitted to the study sites from January 2017 to May 2018 using a structured survey with blood sample collection for PCR analysis and in-depth interviews. Data triangulation of the qualitative and quantitative data was used during analysis. RESULTS International laborers were young (median age 33.0 years IQR 28.0-39.5 years), predominantly male (92%) adults returning mostly from the African continent (84%) who stayed abroad for prolonged periods (median time 13.5 months; IQR 6.0-331.5 months) and were involved in occupations that exposed them to a higher risk of malaria infection. Epidemiological trends were also similar amongst study strands and included the importation of Plasmodium falciparum primarily from African countries and P. vivax from Southeast Asian countries. Of 11 P. malariae and P. ovale infections across two study strands, 10 were imported from the African continent. Participants in the qualitative arm demonstrated limited knowledge about malaria prior to travelling abroad, but reported knowledge transformation through personal or co-worker's experience while abroad. Interestingly, those who had a greater understanding of the severity of malaria presented to the hospital for treatment sooner than those who did not; median of 3 days (IQR 2.0-7.0 days) versus 5 days (IQR 4.0-9.5 days) respectively. CONCLUSION To address the challenges to malaria elimination raised by a growing Vietnamese international labor force, consideration should be given to appropriately targeted interventions and malaria prevention strategies that cover key stages of migration including pre-departure education and awareness, in-country prevention and prophylaxis, and malaria screening upon return.
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Affiliation(s)
| | - Sara Canavati
- Vysnova Partners, Inc., Bethesda, MD USA
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
| | - Hoi Thi Le
- National Hospital for Tropical Diseases, Hanoi, Vietnam
- Hanoi Medical University, Hanoi, Vietnam
| | - Tho Huy Tran
- Parasitology and Entomology (NIMPE), National Institute of Malariology, Hanoi, Vietnam
| | | | - Trung Vu Nguyen
- National Hospital for Tropical Diseases, Hanoi, Vietnam
- Hanoi Medical University, Hanoi, Vietnam
| | - Nga Thi Nguyen
- National Hospital for Tropical Diseases, Hanoi, Vietnam
- Hanoi Medical University, Hanoi, Vietnam
| | - Hoa Mai Tran
- National Hospital for Tropical Diseases, Hanoi, Vietnam
- Hanoi Medical University, Hanoi, Vietnam
| | - Thang Duc Ngo
- Parasitology and Entomology (NIMPE), National Institute of Malariology, Hanoi, Vietnam
| | - Duong Thanh Tran
- Parasitology and Entomology (NIMPE), National Institute of Malariology, Hanoi, Vietnam
| | - Binh Thi Huong Nguyen
- Parasitology and Entomology (NIMPE), National Institute of Malariology, Hanoi, Vietnam
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Sudo M, Osakabe M. freqpcr: Estimation of population allele frequency using qPCR ΔΔCq measures from bulk samples. Mol Ecol Resour 2022; 22:1380-1393. [PMID: 34882971 PMCID: PMC9300209 DOI: 10.1111/1755-0998.13554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022]
Abstract
PCR techniques, both quantitative (qPCR) and nonquantitative, have been used to estimate the frequency of a specific allele in a population. However, the labour required to sample numerous individuals and subsequently handle each sample renders the quantification of rare mutations (e.g., pesticide resistance gene mutations at the early stages of resistance development) challenging. Meanwhile, pooling DNA from multiple individuals as a "bulk sample" combined with qPCR may reduce handling costs. The qPCR output for a bulk sample, however, contains uncertainty owing to variations in DNA yields from each individual, in addition to measurement errors. In this study, we have developed a statistical model to estimate the frequency of the specific allele and its confidence interval when the sample allele frequencies are obtained in the form of ΔΔCq in the qPCR analyses on multiple bulk samples collected from a population. We assumed a gamma distribution as the individual DNA yield and developed an R package for parameter estimation, which was verified using real DNA samples from acaricide-resistant spider mites, as well as a numerical simulation. Our model resulted in unbiased point estimates of the allele frequency compared with simple averaging of the ΔΔCq values. The confidence intervals suggest that dividing the bulk samples into more parts will improve precision if the total number of individuals is equal; however, if the cost of PCR analysis is higher than that of sampling, increasing the total number and pooling them into a few bulk samples may also yield comparable precision.
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Affiliation(s)
- Masaaki Sudo
- Division of Fruit Tree and Tea Pest Control ResearchInstitute for Plant ProtectionNARO: Kanaya Tea Research StationShimadaJapan
| | - Masahiro Osakabe
- Laboratory of Ecological InformationGraduate School of AgricultureKyoto UniversityKyotoJapan
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Escobar M, Jeanneret G, Bravo-Sánchez L, Castillo A, Gómez C, Valderrama D, Roa M, Martínez J, Madrid-Wolff J, Cepeda M, Guevara-Suarez M, Sarmiento OL, Medaglia AL, Forero-Shelton M, Velasco M, Pedraza JM, Laajaj R, Restrepo S, Arbelaez P. Smart pooling: AI-powered COVID-19 informative group testing. Sci Rep 2022; 12:6519. [PMID: 35444162 PMCID: PMC9020431 DOI: 10.1038/s41598-022-10128-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/15/2022] [Indexed: 11/09/2022] Open
Abstract
Massive molecular testing for COVID-19 has been pointed out as fundamental to moderate the spread of the pandemic. Pooling methods can enhance testing efficiency, but they are viable only at low incidences of the disease. We propose Smart Pooling, a machine learning method that uses clinical and sociodemographic data from patients to increase the efficiency of informed Dorfman testing for COVID-19 by arranging samples into all-negative pools. To do this, we ran an automated method to train numerous machine learning models on a retrospective dataset from more than 8000 patients tested for SARS-CoV-2 from April to July 2020 in Bogotá, Colombia. We estimated the efficiency gains of using the predictor to support Dorfman testing by simulating the outcome of tests. We also computed the attainable efficiency gains of non-adaptive pooling schemes mathematically. Moreover, we measured the false-negative error rates in detecting the ORF1ab and N genes of the virus in RT-qPCR dilutions. Finally, we presented the efficiency gains of using our proposed pooling scheme on proof-of-concept pooled tests. We believe Smart Pooling will be efficient for optimizing massive testing of SARS-CoV-2.
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Affiliation(s)
- María Escobar
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, Colombia
| | - Guillaume Jeanneret
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, Colombia
| | - Laura Bravo-Sánchez
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, Colombia
| | - Angela Castillo
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, Colombia
| | - Catalina Gómez
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, Colombia.,Department of Computer Science, Johns Hopkins University, Baltimore, USA
| | - Diego Valderrama
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, Colombia
| | - Mafe Roa
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, Colombia
| | - Julián Martínez
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, Colombia
| | - Jorge Madrid-Wolff
- Laboratory of Applied Photonics Devices, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Martha Cepeda
- School of Science, Universidad de los Andes, Bogotá, Colombia
| | - Marcela Guevara-Suarez
- Applied Genomics Research Group, Vice Presidency for Research and Creation, Universidad de los Andes, Bogotá, Colombia
| | | | - Andrés L Medaglia
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, Colombia.,Department of Industrial Engineering, Universidad de los Andes, Bogotá, Colombia
| | | | - Mauricio Velasco
- Department of Mathematics, Universidad de los Andes, Bogotá, Colombia
| | - Juan M Pedraza
- Department of Physics, Universidad de los Andes, Bogotá, Colombia
| | - Rachid Laajaj
- School of Economics, Universidad de los Andes, Bogotá, Colombia
| | - Silvia Restrepo
- Applied Genomics Research Group, Vice Presidency for Research and Creation, Universidad de los Andes, Bogotá, Colombia
| | - Pablo Arbelaez
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, Colombia. .,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, Colombia.
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14
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Fitri LE, Widaningrum T, Endharti AT, Prabowo MH, Winaris N, Nugraha RYB. Malaria diagnostic update: From conventional to advanced method. J Clin Lab Anal 2022; 36:e24314. [PMID: 35247002 PMCID: PMC8993657 DOI: 10.1002/jcla.24314] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Update diagnostic methods play essential roles in dealing with the current global malaria situation and decreasing malaria incidence. AIM Global malaria control programs require the availability of adequate laboratory tests in the quick and convenient field. RESULTS There are several methods to find out the existence of parasites within the blood. The oldest one is by microscopy, which is still a gold standard, although rapid diagnostic tests (RDTs) have rapidly become a primary diagnostic test in many endemic areas. Because of microscopy and RDTs limitation, novel serological and molecular methods have been developed. Many kinds of polymerase chain reaction (PCR) provide rapid results and higher specificity and sensitivity. The loop-mediated isothermal amplification (LAMP) and biosensing-based molecular techniques as point of care tests (POCT) will become a cost-effective approach to advance diagnostic testing. CONCLUSION Despite conventional techniques are still being used in the field, the exploration and field implementation of advanced techniques for the diagnosis of malaria are still being developed rapidly.
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Affiliation(s)
- Loeki Enggar Fitri
- Department of ParasitologyFaculty of Medicine Universitas BrawijayaMalangIndonesia
- Malaria Research GroupFaculty of Medicine Universitas BrawijayaMalangIndonesia
| | - Tarina Widaningrum
- Malaria Research GroupFaculty of Medicine Universitas BrawijayaMalangIndonesia
- Department of PharmacologyFaculty of Medicine Universitas BrawijayaMalangIndonesia
| | | | | | - Nuning Winaris
- Department of ParasitologyFaculty of Medicine Universitas BrawijayaMalangIndonesia
- Malaria Research GroupFaculty of Medicine Universitas BrawijayaMalangIndonesia
| | - Rivo Yudhinata Brian Nugraha
- Department of ParasitologyFaculty of Medicine Universitas BrawijayaMalangIndonesia
- Malaria Research GroupFaculty of Medicine Universitas BrawijayaMalangIndonesia
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15
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Allam U, Polu VP, Kota NK, Karumanchi D, Basireddy S, Munagapati S, Mugudalabetta S, Ganta V. Evaluation of detection of severe acute respiratory syndrome coronavirus-2 by chip-based real-time polymerase chain reaction test (truenat™ beta CoV) in multi-sample pools. INTERNATIONAL JOURNAL OF ACADEMIC MEDICINE 2022. [DOI: 10.4103/ijam.ijam_14_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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16
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Hajialiani F, Shahbazzadeh D, Maleki F, Elmi T, Tabatabaie F, Zamani Z. The Metabolomic Profiles of Sera of Mice Infected with Plasmodium berghei and Treated by Effective Fraction of Naja naja oxiana Using 1H Nuclear Magnetic Resonance Spectroscopy. Acta Parasitol 2021; 66:1517-1527. [PMID: 34357584 DOI: 10.1007/s11686-021-00456-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND The use of venom fractions from the Iranian cobra could be useful adjunct treatments of malaria with chloroquine. A metabolomic investigation with 1HNMR spectroscopy was conducted on an effective fraction tested earlier using Plasmodium berghei as an experimental murine model. PURPOSE We sought to ascertain both safety and anti-parasitic effects of experimental therapies. METHODS After purification of the venom fractions, 25 mice were infected, then treated for 4 days with 0.2 ml of 5 mg/kg, 2.5 mg/kg and 1 mg/kg of the effective fraction, chloroquine, and a drug vehicle. An ED50 was obtained using Giemsa staining and real-time PCR analysis. The toxicity tests inspecting both liver and kidney tissues were performed. RESULTS A clear inhibitory effect on parasitaemia was observed (with 75% inhibition with 5 mg/kg and 50% reduction when 2.5 mg/kg dosage used). ED50 obtained 2.5 mg/kg. The metabolomics were identified as differentiation of aminoacyl-t-RNA biosynthesis, valine, leucine, isoleucine biosynthesis and degradation pathways were observed. CONCLUSION Upon therapeutic effects of cobra venom fraction, further optimization of dose-dependent response of pharmacokinetics would be worthwhile for further exploration in adjunct experimental venom therapies.
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17
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Improvement of Sensitivity of Pooling Strategies for COVID-19. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:6636396. [PMID: 34691239 PMCID: PMC8528573 DOI: 10.1155/2021/6636396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 07/05/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022]
Abstract
Group testing (or pool testing), for example, Dorfman's method or grid method, has been validated for COVID-19 RT-PCR tests and implemented widely by most laboratories in many countries. These methods take advantages since they reduce resources, time, and overall costs required for a large number of samples. However, these methods could have more false negative cases and lower sensitivity. In order to maintain both accuracy and efficiency for different prevalence, we provide a novel pooling strategy based on the grid method with an extra pool set and an optimized rule inspired by the idea of error-correcting codes. The mathematical analysis shows that (i) the proposed method has the best sensitivity among all the methods we compared, if the false negative rate (FNR) of an individual test is in the range [1%, 20%] and the FNR of a pool test is closed to that of an individual test, and (ii) the proposed method is efficient when the prevalence is below 10%. Numerical simulations are also performed to confirm the theoretical derivations. In summary, the proposed method is shown to be felicitous under the above conditions in the epidemic.
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18
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Daniel EA, Esakialraj L BH, S A, Muthuramalingam K, Karunaianantham R, Karunakaran LP, Nesakumar M, Selvachithiram M, Pattabiraman S, Natarajan S, Tripathy SP, Hanna LE. Pooled Testing Strategies for SARS-CoV-2 diagnosis: A comprehensive review. Diagn Microbiol Infect Dis 2021; 101:115432. [PMID: 34175613 PMCID: PMC8127528 DOI: 10.1016/j.diagmicrobio.2021.115432] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/09/2021] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 has surged across the globe causing the ongoing COVID-19 pandemic. Systematic testing to facilitate index case isolation and contact tracing is needed for efficient containment of viral spread. The major bottleneck in leveraging testing capacity has been the lack of diagnostic resources. Pooled testing is a potential approach that could reduce cost and usage of test kits. This method involves pooling individual samples and testing them 'en bloc'. Only if the pool tests positive, retesting of individual samples is performed. Upon reviewing recent articles on this strategy employed in various SARS-CoV-2 testing scenarios, we found substantial diversity emphasizing the requirement of a common protocol. In this article, we review various theoretically simulated and clinically validated pooled testing models and propose practical guidelines on applying this strategy for large scale screening. If implemented properly, the proposed approach could contribute to proper utilization of testing resources and flattening of infection curve.
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Affiliation(s)
- Evangeline Ann Daniel
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India.
| | | | - Anbalagan S
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | | | | | | | - Manohar Nesakumar
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | | | | | - Sudhakar Natarajan
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | | | - Luke Elizabeth Hanna
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India.
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19
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Barlow A, Roy K, Hawkins K, Ankarah AA, Rosenthal B. A review of testing and assurance methods for Trichinella surveillance programs. Food Waterborne Parasitol 2021; 24:e00129. [PMID: 34458599 PMCID: PMC8379475 DOI: 10.1016/j.fawpar.2021.e00129] [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] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 11/26/2022] Open
Abstract
While global cases of trichinellosis have fallen since pork regulation began, the disease remains a danger to pork and animal game consumers as well as a liability to producers. Managing food safety risk and supporting agricultural trade requires cost-effective and sensitive diagnostic methods. Several means exist to inspect pork for parasitic infections. Here, we review literature concerning the sensitivity, specificity, and cost of these methods. We found that artificial digestion coupled with optical microscopy to be the best method for verification of Trichinella larva free pork due to its cost efficiency, high specificity, and reliability. Serological techniques such as ELISA are useful for epidemiological surveillance of swine. While current PCR techniques are quick and useful for diagnosing species-specific infections, they are not cost efficient for large-scale testing. However, as PCR techniques, including Lateral Flow- Recombinase Polymerase Amplification (LF-RPA), improve and continue to reduce cost, such methods may ultimately succeed artificial digestion. We compared cost, sensitivity, and specificity of available and foreseeable tools. The magnetic stir bar method remains the gold standard for Trichinella surveillance. Serological methods miss early infections but offer promise for use in surveillance. Isothermal methods offer future promise given their speed, accuracy, and ease of use. Genetic methods are uneconomical but advances have promise to reduce cost.
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Affiliation(s)
- Alec Barlow
- USDA, ARS, NEA, BARC, Animal Parasitic Diseases Laboratory, Beltsville, MD, United States of America
| | - Kayla Roy
- USDA, ARS, NEA, BARC, Animal Parasitic Diseases Laboratory, Beltsville, MD, United States of America
| | - Kristopher Hawkins
- USDA, ARS, NEA, BARC, Animal Parasitic Diseases Laboratory, Beltsville, MD, United States of America
| | - Ako A Ankarah
- USDA, ARS, NEA, BARC, Animal Parasitic Diseases Laboratory, Beltsville, MD, United States of America
| | - Benjamin Rosenthal
- USDA, ARS, NEA, BARC, Animal Parasitic Diseases Laboratory, Beltsville, MD, United States of America
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20
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Jeong H, Lee J, Cheon S, Sohn KM, Kim J, Kym S, Kim YS. Experimental and Mathematical Optimization of a Pooling Test for Detection of SARS-CoV-2 in a Population with Low Viral Load. Infect Chemother 2021; 53:118-127. [PMID: 34409785 PMCID: PMC8032915 DOI: 10.3947/ic.2021.0005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/03/2021] [Indexed: 01/12/2023] Open
Abstract
Background A pooling test is a useful tool for mass screening of coronavirus disease 2019 (COVID-19) in the pandemic era. We aimed to optimize a simple two-step pooling test by estimating the optimal pool size using experimental and mathematical validation. Materials and Methods Experimental pools were created by mixing one positive respiratory sample with various numbers of negative samples. We selected positive samples with cycle threshold (Ct) values greater than 32 to validate the efficiency of the pooling test assuming a high likelihood of false-negative results due to low viral loads. The positivities of the experimental pools were investigated with a single reverse-transcription polymerase chain reaction (RT-PCR) using the U-TOP™ COVID-19 Detection Kit Plus (Seasun Biomaterials, Daejeon, Korea). We used the Dorfman equation to calculate the optimal size of a pooling test mathematically. Results Viral RNA could be detected in a pool with a size up to 11, even if the Ct value of a positive sample was about 35. The Dorfman equation showed that the optimal number of samples in a pool was 11 when the prevalence was assumed to be 0.66% based on the test positivity in Daejeon, Korea from April 1, 2020 to November 10, 2020. The efficiency of the pooling test was 6.2, which can save 83.9 of 100 individual tests. Conclusion Eleven samples in a pool were validated optimal experimentally assuming a prevalence of 0.66%. The pool size needs modification as the pandemic progresses; thus, the prevalence should be carefully estimated before pooling tests are conducted.
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Affiliation(s)
- Hyeongseok Jeong
- Division of Infectious Disease, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Jooyeon Lee
- Division of Infectious Disease, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Shinhye Cheon
- Division of Infectious Disease, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Kyung Mok Sohn
- Division of Infectious Disease, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Jungok Kim
- Division of Infectious Disease, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Sungmin Kym
- Division of Infectious Disease, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea
| | - Yeon Sook Kim
- Division of Infectious Disease, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea.
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21
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Waldstein KA, Yi J, Cho MM, Mudumbai R, Wu X, Varga SM, Xu W. Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.08.09.21261669. [PMID: 34401889 PMCID: PMC8366810 DOI: 10.1101/2021.08.09.21261669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The rapid spread of SARS-CoV-2 has placed a significant burden on public health systems to provide rapid and accurate diagnostic testing highlighting the critical need for innovative testing approaches for future pandemics. In this study, we present a novel sample pooling procedure based on compressed sensing theory to accurately identify virally infected patients at high prevalence rates utilizing an innovative viral RNA extraction process to minimize sample dilution. At prevalence rates ranging from 0-14.3%, the number of tests required to identify the infection status of all patients was reduced by 75.6% as compared to conventional testing in primary human SARS-CoV-2 nasopharyngeal swabs and a coronavirus model system. Additionally, our modified pooling and RNA extraction process minimized sample dilution which remained constant as pool sizes increased. Our use of compressed sensing can be adapted to a wide variety of diagnostic testing applications to increase throughput for routine laboratory testing as well as a means to increase testing throughput to combat future pandemics.
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Affiliation(s)
- Kody A. Waldstein
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242, USA
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Jirong Yi
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Michael Myung Cho
- Department of Electrical and Computer Engineering, Penn State Behrend, Erie, PA 16563, USA
| | - Raghu Mudumbai
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Xiaodong Wu
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Steven M. Varga
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242, USA
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
| | - Weiyu Xu
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA
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22
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Attia MA, Chang WT, Tandon R. Heterogeneity Aware Two-Stage Group Testing. IEEE TRANSACTIONS ON SIGNAL PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2021; 69:3977-3990. [PMID: 37982073 PMCID: PMC8544931 DOI: 10.1109/tsp.2021.3093785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 02/19/2021] [Accepted: 06/16/2021] [Indexed: 11/21/2023]
Abstract
Group testing refers to the process of testing pooled samples to reduce the total number of tests. Given the current pandemic, and the shortage of test supplies for COVID-19, group testing can play a critical role in time and cost efficient diagnostics. In many scenarios, samples collected from users are also accompanied with auxiliary information (such as demographics, history of exposure, onset of symptoms). Such auxiliary information may differ across patients, and is typically not considered while designing group testing algorithms. In this paper, we abstract such heterogeneity using a model where the population can be categorized into clusters with different prevalence rates. The main result of this work is to show that exploiting knowledge heterogeneity can further improve the efficiency of group testing. Motivated by the practical constraints and diagnostic considerations, we focus on two-stage group testing algorithms, where in the first stage, the goal is to detect as many negative samples by pooling, whereas the second stage involves individual testing to detect any remaining samples. For this class of algorithms, we prove that the gain in efficiency is related to the concavity of the number of tests as a function of the prevalence. We also show how one can choose the optimal pooling parameters for one of the algorithms in this class, namely, doubly constant pooling. We present lower bounds on the average number of tests as a function of the population heterogeneity profile, and also provide numerical results and comparisons.
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Affiliation(s)
- Mohamed A Attia
- Department of Electrical, Computer EngineeringUniversity of Arizona Tucson AZ 85721 USA
| | - Wei-Ting Chang
- Department of Electrical, Computer EngineeringUniversity of Arizona Tucson AZ 85721 USA
| | - Ravi Tandon
- Department of Electrical, Computer EngineeringUniversity of Arizona Tucson AZ 85721 USA
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23
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Sazed SA, Kibria MG, Alam MS. An Optimized Real-Time qPCR Method for the Effective Detection of Human Malaria Infections. Diagnostics (Basel) 2021; 11:736. [PMID: 33919020 PMCID: PMC8142979 DOI: 10.3390/diagnostics11050736] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/24/2022] Open
Abstract
Polymerase chain reaction, although an expensive method for the detection of human Plasmodium spp., is still considered the finest for the diagnosis of malaria. The conventional diagnostic PCR is an inexpensive process but consumes a lot of time, reagents and lacks sensitivity. On the other hand, real-time PCR assays currently being used are mostly probe-based expensive methods and sometimes not feasible to detect all the species in a single amplification reaction condition. Here we have established a real-time PCR method that is time and cost effective with a single protocol to detect and distinguish five human Plasmodium species using the existing primers efficiently. The primers used here are being used in the conventional method and the sensitivity as well as specificity of this method has also been immensely improved (100%). The lower limit of detection for Plasmodium falciparum, Plasmodium vivax and Plasmodium malariae are 0.064 parasites/µL, 1.6 parasites/µL, and 0.32 parasites/µL respectively and no cross reactivity was observed. Besides, we have analyzed melt curves that can be used for further species confirmation and validation purposes using multiplex systems. This method, therefore, can be considered as an alternative to the existing lineup for molecular diagnosis of malaria in endemic countries.
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Affiliation(s)
| | | | - Mohammad Shafiul Alam
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh Mohakhali, Dhaka 1212, Bangladesh; (S.A.S.); (M.G.K.)
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24
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Cleary B, Hay JA, Blumenstiel B, Harden M, Cipicchio M, Bezney J, Simonton B, Hong D, Senghore M, Sesay AK, Gabriel S, Regev A, Mina MJ. Using viral load and epidemic dynamics to optimize pooled testing in resource-constrained settings. Sci Transl Med 2021; 13:eabf1568. [PMID: 33619080 PMCID: PMC8099195 DOI: 10.1126/scitranslmed.abf1568] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/10/2021] [Indexed: 12/17/2022]
Abstract
Virological testing is central to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) containment, but many settings face severe limitations on testing. Group testing offers a way to increase throughput by testing pools of combined samples; however, most proposed designs have not yet addressed key concerns over sensitivity loss and implementation feasibility. Here, we combined a mathematical model of epidemic spread and empirically derived viral kinetics for SARS-CoV-2 infections to identify pooling designs that are robust to changes in prevalence and to ratify sensitivity losses against the time course of individual infections. We show that prevalence can be accurately estimated across a broad range, from 0.02 to 20%, using only a few dozen pooled tests and using up to 400 times fewer tests than would be needed for individual identification. We then exhaustively evaluated the ability of different pooling designs to maximize the number of detected infections under various resource constraints, finding that simple pooling designs can identify up to 20 times as many true positives as individual testing with a given budget. Crucially, we confirmed that our theoretical results can be translated into practice using pooled human nasopharyngeal specimens by accurately estimating a 1% prevalence among 2304 samples using only 48 tests and through pooled sample identification in a panel of 960 samples. Our results show that accounting for variation in sampled viral loads provides a nuanced picture of how pooling affects sensitivity to detect infections. Using simple, practical group testing designs can vastly increase surveillance capabilities in resource-limited settings.
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Affiliation(s)
- Brian Cleary
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - James A Hay
- Centre for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Maegan Harden
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jon Bezney
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brooke Simonton
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David Hong
- Wharton Statistics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Madikay Senghore
- Centre for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Michael J Mina
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Centre for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02120, USA
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25
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Perivolaropoulos C, Vlacha V. A reduction of the number of assays and turnaround time by optimizing polymerase chain reaction (PCR) pooled testing for SARS-CoV-2. J Med Virol 2021; 93:4508-4515. [PMID: 33783005 PMCID: PMC8250672 DOI: 10.1002/jmv.26972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/04/2021] [Accepted: 03/24/2021] [Indexed: 01/07/2023]
Abstract
Early detection of the severe acute respiratory syndrome coronavirus 2 infection can decrease the spread of the disease and provide therapeutic options promptly in affected individuals. However, the diagnosis by reverse‐transcription polymerase chain reaction is costly and time‐consuming. Several methods of group testing have been developed to overcome this problem. The proposed strategy offers optimization of group testing according to the available resources by decreasing not only the number of the assays but also the turnaround time. The initial classification of the samples would be done according to the intention of testing defined as diagnostic or screening/surveillance, achieving the best possible homogeneity. The proposed stratification of pooling is based on branching (divisions) and depth (levels of re‐pooling) of the original group in association with the estimated probability of a positive sample. The dilutional effect of the grouped samples has also been considered. The margins of minimum and maximum conservation of assays of pooled specimens are calculated and the optimum strategy can be selected in association with the probability of positive samples in the original group. This algorithm intends to be a useful tool for group testing offering a choice of strategies according to the requirements.
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Affiliation(s)
| | - Vasiliki Vlacha
- Department of Early Years Learning and Care, University of Ioannina, Ioannina, Greece.,Paediatric Department, Karamandanio Children's Hospital of Patras, Patras, Greece
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26
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Ultrasensitive Diagnostics for Low-Density Asymptomatic Plasmodium falciparum Infections in Low-Transmission Settings. J Clin Microbiol 2021; 59:JCM.01508-20. [PMID: 33148707 DOI: 10.1128/jcm.01508-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The emergence of multidrug-resistant Plasmodium falciparum malaria in Southeast Asia (SEA) has accelerated regional malaria elimination efforts. Most malaria in this and other low-transmission settings exists in asymptomatic individuals, which conventional diagnostic tests lack the sensitivity to detect. This has led to the development of new ultrasensitive diagnostics that are capable of detecting these low-parasitemia infections. This review summarizes the current status of ultrasensitive technologies, including PCR and loop-mediated isothermal amplification (LAMP)-based methods, as well as a newly developed ultrasensitive rapid diagnostic test (uRDT). The sensitivity, specificity, and field performance of these platforms will be examined, as well as their suitability for use in resource-limited settings to aid in malaria elimination efforts. uRDTs, with their improved sensitivity, are now able to detect approximately half of asymptomatic infections, providing a useful point-of-contact tool for malaria surveillance. The increased sensitivity and high-throughput nature of PCR-based tests make them ideal for screening large populations in places where laboratory capacity exists, and the recent commercialization of malaria LAMP kits should facilitate their adoption as a public health tool in places where such infrastructure is lacking. Finally, recent advances with dried blood spots may enable utilization of the extensive laboratory infrastructure of higher-income countries to assist with molecular surveillance in support of malaria elimination. If malaria is to be eliminated in SEA and other low-endemicity regions, then ultrasensitive diagnostics will likely play a key role in identifying and clearing the vast asymptomatic pool of infections that are common to these regions.
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Selection of Cytochrome b Mutants Is Rare among Plasmodium falciparum Patients Failing Treatment with Atovaquone-Proguanil in Cambodia. Antimicrob Agents Chemother 2021; 65:AAC.01249-20. [PMID: 33361308 DOI: 10.1128/aac.01249-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/18/2020] [Indexed: 11/20/2022] Open
Abstract
Atovaquone-proguanil remains effective against multidrug-resistant Plasmodium falciparum in Southeast Asia, but resistance is mediated by a single point mutation in cytochrome b (cytb) that can arise during treatment. Among 14 atovaquone-proguanil treatment failures in a clinical trial in Cambodia, only one recrudescence harbored the cytb mutation Y268C. Deep sequencing did not detect the mutation at baseline or in the first 3 days of treatment, suggesting that it arose de novo Further sequencing across cytb similarly found no low-frequency cytb mutations that were up-selected from baseline to recrudescence. Copy number amplification in dihydroorotate dehydrogenase (DHODH) and cytb as markers of atovaquone tolerance was also absent. Cytb mutation played a minor role in atovaquone-proguanil treatment failures in an active comparator clinical trial.
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Markwalter CF, Ngasala B, Mowatt T, Basham C, Park Z, Loya M, Muller M, Plowe C, Nyunt M, Lin JT. Direct Comparison of Standard and Ultrasensitive PCR for the Detection of Plasmodium falciparum from Dried Blood Spots in Bagamoyo, Tanzania. Am J Trop Med Hyg 2021; 104:1371-1374. [PMID: 33556035 DOI: 10.4269/ajtmh.20-1233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/29/2020] [Indexed: 11/07/2022] Open
Abstract
Ultrasensitive PCR used in low-transmission malaria-endemic settings has revealed a much higher burden of asymptomatic infections than that detected by rapid diagnostic tests (RDTs) or standard PCR, but there is limited evidence as to whether this is the case in higher transmission settings. Using dried blood spots (DBS) collected among 319 schoolchildren in Bagamoyo, Tanzania, we found good correlation (Pearson's R = 0.995) between Plasmodium falciparum parasite densities detected by a DNA-based 18s rRNA real-time PCR (qPCR) and an RNA-based ultrasensitive RT-PCR (usPCR) for the same target. Whereas prevalence by usPCR was higher than that found by qPCR (37% versus 32%), the proportion of additionally detected low-density infections (median parasite density < 0.050 parasites/µL) represented an incremental increase. It remains unclear to what extent these low-density infections may contribute to the infectious reservoir in different malaria transmission settings.
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Affiliation(s)
| | - Billy Ngasala
- 2Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Tonelia Mowatt
- 1Duke Global Health Institute, Duke University, Durham, North Carolina
| | - Christopher Basham
- 3Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Zackary Park
- 3Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Mwajabu Loya
- 2Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Meredith Muller
- 3Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | | | - Myaing Nyunt
- 4University of Maryland School of Medicine, Baltimore, Maryland
| | - Jessica T Lin
- 3Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina
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Cleary B, Hay JA, Blumenstiel B, Harden M, Cipicchio M, Bezney J, Simonton B, Hong D, Senghore M, Sesay AK, Gabriel S, Regev A, Mina MJ. Using viral load and epidemic dynamics to optimize pooled testing in resource constrained settings. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.05.01.20086801. [PMID: 32511487 PMCID: PMC7273255 DOI: 10.1101/2020.05.01.20086801] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Extensive virological testing is central to SARS-CoV-2 containment, but many settings face severe limitations on testing. Group testing offers a way to increase throughput by testing pools of combined samples; however, most proposed designs have not yet addressed key concerns over sensitivity loss and implementation feasibility. Here, we combine a mathematical model of epidemic spread and empirically derived viral kinetics for SARS-CoV-2 infections to identify pooling designs that are robust to changes in prevalence, and to ratify losses in sensitivity against the time course of individual infections. Using this framework, we show that prevalence can be accurately estimated across four orders of magnitude using only a few dozen pooled tests without the need for individual identification. We then exhaustively evaluate the ability of different pooling designs to maximize the number of detected infections under various resource constraints, finding that simple pooling designs can identify up to 20 times as many positives compared to individual testing with a given budget. We illustrate how pooling affects sensitivity and overall detection capacity during an epidemic and on each day post infection, finding that sensitivity loss is mainly attributed to individuals sampled at the end of infection when detection for public health containment has minimal benefit. Crucially, we confirm that our theoretical results can be accurately translated into practice using pooled human nasopharyngeal specimens. Our results show that accounting for variation in sampled viral loads provides a nuanced picture of how pooling affects sensitivity to detect epidemiologically relevant infections. Using simple, practical group testing designs can vastly increase surveillance capabilities in resource-limited settings.
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Affiliation(s)
- Brian Cleary
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - James A. Hay
- Centre for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health
| | | | - Maegan Harden
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | | | - Jon Bezney
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | | | - David Hong
- Wharton Statistics, University of Pennsylvania, Philadelphia, PA, USA
| | - Madikay Senghore
- Centre for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Abdul K. Sesay
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142 USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Michael J. Mina
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Centre for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School
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Allah HMA, Abdo E, Elamin EAE, Abdelghani S, Eltayeb LB. Molecular Screening for Transfusion Transmissible P. falciparum in Asymptomatic Blood Donors in the Non-endemic Region. JOURNAL OF BIOCHEMICAL TECHNOLOGY 2021; 12:6-10. [DOI: 10.51847/d8p0p9b063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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31
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Yelin I, Aharony N, Tamar ES, Argoetti A, Messer E, Berenbaum D, Shafran E, Kuzli A, Gandali N, Shkedi O, Hashimshony T, Mandel-Gutfreund Y, Halberthal M, Geffen Y, Szwarcwort-Cohen M, Kishony R. Evaluation of COVID-19 RT-qPCR Test in Multi sample Pools. Clin Infect Dis 2020; 71:2073-2078. [PMID: 32358960 PMCID: PMC7197588 DOI: 10.1093/cid/ciaa531] [Citation(s) in RCA: 262] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/30/2020] [Indexed: 11/28/2022] Open
Abstract
Background The recent emergence of SARS-CoV-2 lead to a current pandemic of unprecedented scale. Though diagnostic tests are fundamental to the ability to detect and respond, overwhelmed healthcare systems are already experiencing shortages of reagents associated with this test, calling for a lean immediately-applicable protocol. Methods RNA extracts of positive samples were tested for the presence of SARS-CoV-2 using RT-qPCR, alone or in pools of different sizes (2-, 4-, 8- ,16-, 32- and 64-sample pools) with negative samples. Transport media of additional 3 positive samples were also tested when mixed with transport media of negative samples in pools of 8. Results A single positive sample can be detected in pools of up to 32 samples, using the standard kits and protocols, with an estimated false negative rate of 10%. Detection of positive samples diluted in even up to 64 samples may also be attainable, though may require additional amplification cycles. Single positive samples can be detected when pooling either after or prior to RNA extraction. Conclusions As it uses the standard protocols, reagents and equipment, this pooling method can be applied immediately in current clinical testing laboratories. We hope that such implementation of a pool test for COVID-19 would allow expanding current screening capacities thereby enabling the expansion of detection in the community, as well as in close organic groups, such as hospital departments, army units, or factory shifts.
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Affiliation(s)
- Idan Yelin
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Noga Aharony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Einat Shaer Tamar
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Esther Messer
- Safety Unit, Technion - Israel Institute of Technology, Haifa, Israel
| | - Dina Berenbaum
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Einat Shafran
- Virology laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Areen Kuzli
- Virology laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Nagham Gandali
- Virology laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Omer Shkedi
- Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.,Computer Science Department, Technion - Israel Institute of Technology, Haifa, Israel
| | - Michael Halberthal
- Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.,Rambam Health Care Campus, Haifa, Israel
| | - Yuval Geffen
- Bacteriology laboratory, Rambam Health Care Campus, Haifa, Israel
| | | | - Roy Kishony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.,Computer Science Department, Technion - Israel Institute of Technology, Haifa, Israel
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32
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Tan JG, Omar A, Lee WBY, Wong MS. Considerations for Group Testing: A Practical Approach for the Clinical Laboratory. Clin Biochem Rev 2020; 41:79-92. [PMID: 33343043 PMCID: PMC7731934 DOI: 10.33176/aacb-20-00007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Group testing, also known as pooled sample testing, was first proposed by Robert Dorfman in 1943. While sample pooling has been widely practiced in blood-banking, it is traditionally seen as anathema for clinical laboratories. However, the ongoing COVID-19 pandemic has re-ignited interest for group testing among clinical laboratories to mitigate supply shortages. We propose five criteria to assess the suitability of an analyte for pooled sample testing in general and outline a practical approach that a clinical laboratory may use to implement pooled testing for SARS-CoV-2 PCR testing. The five criteria we propose are: (1) the analyte concentrations in the diseased persons should be at least one order of magnitude (10 times) higher than in healthy persons; (2) sample dilution should not overly reduce clinical sensitivity; (3) the current prevalence must be sufficiently low for the number of samples pooled for the specific protocol; (4) there is no requirement for a fast turnaround time; and (5) there is an imperative need for resource rationing to maximise public health outcomes. The five key steps we suggest for a successful implementation are: (1) determination of when pooling takes place (pre-pre analytical, pre-analytical, analytical); (2) validation of the pooling protocol; (3) ensuring an adequate infrastructure and archival system; (4) configuration of the laboratory information system; and (5) staff training. While pool testing is not a panacea to overcome reagent shortage, it may allow broader access to testing but at the cost of reduction in sensitivity and increased turnaround time.
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Affiliation(s)
- Jun G Tan
- Department of Laboratory Medicine, Khoo Teck Puat Hospital, Singapore
| | - Aznan Omar
- Department of Laboratory Medicine, Khoo Teck Puat Hospital, Singapore
| | - Wendy BY Lee
- Department of Laboratory Medicine, Khoo Teck Puat Hospital, Singapore
| | - Moh S Wong
- Department of Laboratory Medicine, Khoo Teck Puat Hospital, Singapore
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33
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Yelin I, Aharony N, Tamar ES, Argoetti A, Messer E, Berenbaum D, Shafran E, Kuzli A, Gandali N, Shkedi O, Hashimshony T, Mandel-Gutfreund Y, Halberthal M, Geffen Y, Szwarcwort-Cohen M, Kishony R. Evaluation of COVID-19 RT-qPCR Test in Multi sample Pools. Clin Infect Dis 2020. [PMID: 32358960 DOI: 10.1101/2020.03.26.20039438] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to a current pandemic of unprecedented scale. Although diagnostic tests are fundamental to the ability to detect and respond, overwhelmed healthcare systems are already experiencing shortages of reagents associated with this test, calling for a lean immediately applicable protocol. METHODS RNA extracts of positive samples were tested for the presence of SARS-CoV-2 using reverse transcription quantitative polymerase chain reaction, alone or in pools of different sizes (2-, 4-, 8-, 16-, 32-, and 64-sample pools) with negative samples. Transport media of additional 3 positive samples were also tested when mixed with transport media of negative samples in pools of 8. RESULTS A single positive sample can be detected in pools of up to 32 samples, using the standard kits and protocols, with an estimated false negative rate of 10%. Detection of positive samples diluted in even up to 64 samples may also be attainable, although this may require additional amplification cycles. Single positive samples can be detected when pooling either after or prior to RNA extraction. CONCLUSIONS As it uses the standard protocols, reagents, and equipment, this pooling method can be applied immediately in current clinical testing laboratories. We hope that such implementation of a pool test for coronavirus disease 2019 would allow expanding current screening capacities, thereby enabling the expansion of detection in the community, as well as in close organic groups, such as hospital departments, army units, or factory shifts.
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Affiliation(s)
- Idan Yelin
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Noga Aharony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Einat Shaer Tamar
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Esther Messer
- Safety Unit, Technion - Israel Institute of Technology, Haifa, Israel
| | - Dina Berenbaum
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Einat Shafran
- Virology laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Areen Kuzli
- Virology laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Nagham Gandali
- Virology laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Omer Shkedi
- Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
- Computer Science Department, Technion - Israel Institute of Technology, Haifa, Israel
| | - Michael Halberthal
- Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Rambam Health Care Campus, Haifa, Israel
| | - Yuval Geffen
- Bacteriology laboratory, Rambam Health Care Campus, Haifa, Israel
| | | | - Roy Kishony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
- Computer Science Department, Technion - Israel Institute of Technology, Haifa, Israel
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34
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Furstenau TN, Cocking JH, Hepp CM, Fofanov VY. Sample pooling methods for efficient pathogen screening: Practical implications. PLoS One 2020; 15:e0236849. [PMID: 33175841 PMCID: PMC7657563 DOI: 10.1371/journal.pone.0236849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/14/2020] [Indexed: 01/06/2023] Open
Abstract
Due to the large number of negative tests, individually screening large populations for rare pathogens can be wasteful and expensive. Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categorize positive and negative individuals. Such methods rely on group testing theory which mainly focuses on minimizing the total number of tests; however, many other practical concerns and tradeoffs must be considered when choosing an appropriate method for a given set of circumstances. Here we use computational simulations to determine how several theoretical approaches compare in terms of (a) the number of tests, to minimize costs and save reagents, (b) the number of sequential steps, to reduce the time it takes to complete the assay, (c) the number of samples per pool, to avoid the limits of detection, (d) simplicity, to reduce the risk of human error, and (e) robustness, to poor estimates of the number of positive samples. We found that established methods often perform very well in one area but very poorly in others. Therefore, we introduce and validate a new method which performs fairly well across each of the above criteria making it a good general use approach.
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Affiliation(s)
- Tara N. Furstenau
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jill H. Cocking
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Crystal M. Hepp
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Viacheslav Y. Fofanov
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
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Abid S, Ferjani S, El Moussi A, Ferjani A, Nasr M, Landolsi I, Saidi K, Gharbi H, Letaief H, Hechaichi A, Safer M, Ben Alaya NBE, Boubaker IBB. Assessment of sample pooling for SARS-CoV-2 molecular testing for screening of asymptomatic persons in Tunisia. Diagn Microbiol Infect Dis 2020; 98:115125. [PMID: 32768876 PMCID: PMC7335417 DOI: 10.1016/j.diagmicrobio.2020.115125] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/03/2022]
Abstract
The aim of this study is to test a pooling approach for the RT-PCR test to detect low viral loads of SARS-CoV-2. We found that a single positive specimen can still be detected in pools of up to 10. Each laboratory should conduct its own evaluation and validation of pooling protocols according to its specific context.
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Affiliation(s)
- Salma Abid
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
| | - Sana Ferjani
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia.
| | - Awatef El Moussi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
| | - Asma Ferjani
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
| | - Mejda Nasr
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Ichrak Landolsi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Karima Saidi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Hanène Gharbi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Hajer Letaief
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006, Tunis, Tunisia
| | - Aicha Hechaichi
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006, Tunis, Tunisia
| | - Mouna Safer
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006, Tunis, Tunisia
| | | | - Ilhem Boutiba-Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
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Topazian HM, Gumbo A, Puerto-Meredith S, Njiko R, Mwanza A, Kayange M, Mwalilino D, Mvula B, Tegha G, Mvalo T, Edwards JK, Emch M, Pettifor A, Smith JS, Hoffman I, Meshnick SR, Juliano JJ. Asymptomatic Plasmodium falciparum malaria prevalence among adolescents and adults in Malawi, 2015-2016. Sci Rep 2020; 10:18740. [PMID: 33127922 PMCID: PMC7603306 DOI: 10.1038/s41598-020-75261-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/13/2020] [Indexed: 11/25/2022] Open
Abstract
Malaria remains a significant cause of morbidity and mortality in Malawi, with an estimated 18–19% prevalence of Plasmodium falciparum in children 2–10 years in 2015–2016. While children report the highest rates of clinical disease, adults are thought to be an important reservoir to sustained transmission due to persistent asymptomatic infection. The 2015–2016 Malawi Demographic and Health Survey was a nationally representative household survey which collected dried blood spots from 15,125 asymptomatic individuals ages 15–54 between October 2015 and February 2016. We performed quantitative polymerase chain reaction on 7,393 samples, detecting an overall P. falciparum prevalence of 31.1% (SE = 1.1). Most infections (55.6%) had parasitemias ≤ 10 parasites/µL. While 66.2% of individuals lived in a household that owned a bed net, only 36.6% reported sleeping under a long-lasting insecticide-treated net (LLIN) the previous night. Protective factors included urbanicity, greater wealth, higher education, and lower environmental temperatures. Living in a household with a bed net (prevalence difference 0.02, 95% CI − 0.02 to 0.05) and sleeping under an LLIN (0.01; − 0.02 to 0.04) were not protective against infection. Our findings demonstrate a higher parasite prevalence in adults than published estimates among children. Understanding the prevalence and distribution of asymptomatic infection is essential for targeted interventions.
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Affiliation(s)
- Hillary M Topazian
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27510, USA.
| | - Austin Gumbo
- National Malaria Control Programme, Malawi Ministry of Health, Lilongwe, Malawi
| | | | - Ruth Njiko
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Alexis Mwanza
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27510, USA
| | - Michael Kayange
- National Malaria Control Programme, Malawi Ministry of Health, Lilongwe, Malawi
| | - David Mwalilino
- National HIV Reference Laboratory, Malawi Ministry of Health, Lilongwe, Malawi
| | - Bernard Mvula
- National HIV Reference Laboratory, Malawi Ministry of Health, Lilongwe, Malawi
| | - Gerald Tegha
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Tisungane Mvalo
- University of North Carolina Project-Malawi, Lilongwe, Malawi.,Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Jessie K Edwards
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27510, USA
| | - Michael Emch
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27510, USA.,Department of Geography, University of North Carolina, Chapel Hill, NC, USA
| | - Audrey Pettifor
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27510, USA.,Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jennifer S Smith
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27510, USA
| | - Irving Hoffman
- University of North Carolina Project-Malawi, Lilongwe, Malawi.,Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Steven R Meshnick
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27510, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
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Deckert A, Bärnighausen T, Kyei NN. Simulation of pooled-sample analysis strategies for COVID-19 mass testing. Bull World Health Organ 2020; 98:590-598. [PMID: 33012859 PMCID: PMC7463190 DOI: 10.2471/blt.20.257188] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 01/24/2023] Open
Abstract
OBJECTIVE To evaluate two pooled-sample analysis strategies (a routine high-throughput approach and a novel context-sensitive approach) for mass testing during the coronavirus disease 2019 (COVID-19) pandemic, with an emphasis on the number of tests required to screen a population. METHODS We used Monte Carlo simulations to compare the two testing strategies for different infection prevalences and pooled group sizes. With the routine high-throughput approach, heterogeneous sample pools are formed randomly for polymerase chain reaction (PCR) analysis. With the novel context-sensitive approach, PCR analysis is performed on pooled samples from homogeneous groups of similar people that have been purposively formed in the field. In both approaches, all samples contributing to pools that tested positive are subsequently analysed individually. FINDINGS Both pooled-sample strategies would save substantial resources compared to individual analysis during surge testing and enhanced epidemic surveillance. The context-sensitive approach offers the greatest savings: for instance, 58-89% fewer tests would be required for a pooled group size of 3 to 25 samples in a population of 150 000 with an infection prevalence of 1% or 5%. Correspondingly, the routine high-throughput strategy would require 24-80% fewer tests than individual testing. CONCLUSION Pooled-sample PCR screening could save resources during COVID-19 mass testing. In particular, the novel context-sensitive approach, which uses pooled samples from homogeneous population groups, could substantially reduce the number of tests required to screen a population. Pooled-sample approaches could help countries sustain population screening over extended periods of time and thereby help contain foreseeable second-wave outbreaks.
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Affiliation(s)
- Andreas Deckert
- Heidelberg Institute of Global Health, Heidelberg University, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Till Bärnighausen
- Heidelberg Institute of Global Health, Heidelberg University, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Nicholas Na Kyei
- Heidelberg Institute of Global Health, Heidelberg University, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
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38
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Goupeyou-Youmsi J, Rakotondranaivo T, Puchot N, Peterson I, Girod R, Vigan-Womas I, Paul R, Ndiath MO, Bourgouin C. Differential contribution of Anopheles coustani and Anopheles arabiensis to the transmission of Plasmodium falciparum and Plasmodium vivax in two neighbouring villages of Madagascar. Parasit Vectors 2020; 13:430. [PMID: 32843082 PMCID: PMC7447585 DOI: 10.1186/s13071-020-04282-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 08/03/2020] [Indexed: 02/01/2023] Open
Abstract
Background Malaria is still a heavy public health concern in Madagascar. Few studies combining parasitology and entomology have been conducted despite the need for accurate information to design effective vector control measures. In a Malagasy region of moderate to intense transmission of both Plasmodium falciparum and P. vivax, parasitology and entomology have been combined to survey malaria transmission in two nearby villages. Methods Community-based surveys were conducted in the villages of Ambohitromby and Miarinarivo at three time points (T1, T2 and T3) during a single malaria transmission season. Human malaria prevalence was determined by rapid diagnostic tests (RDTs), microscopy and real-time PCR. Mosquitoes were collected by human landing catches and pyrethrum spray catches and the presence of Plasmodium sporozoites was assessed by TaqMan assay. Results Malaria prevalence was not significantly different between villages, with an average of 8.0% by RDT, 4.8% by microscopy and 11.9% by PCR. This was mainly due to P. falciparum and to a lesser extent to P. vivax. However, there was a significantly higher prevalence rate as determined by PCR at T2 (\documentclass[12pt]{minimal}
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\begin{document}$$\chi_{2}^{2}$$\end{document}χ22 = 7.46, P = 0.025). Likewise, mosquitoes were significantly more abundant at T2 (\documentclass[12pt]{minimal}
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\begin{document}$$\chi_{2}^{2}$$\end{document}χ22 = 64.8, P < 0.001), especially in Ambohitromby. At T1 and T3 mosquito abundance was higher in Miarinarivo than in Ambohitromby (\documentclass[12pt]{minimal}
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\begin{document}$$\chi_{2}^{2}$$\end{document}χ22 = 14.92, P < 0.001). Of 1550 Anopheles mosquitoes tested, 28 (1.8%) were found carrying Plasmodium sporozoites. The entomological inoculation rate revealed that Anopheles coustani played a major contribution in malaria transmission in Miarinarivo, being responsible of 61.2 infective bites per human (ib/h) during the whole six months of the survey, whereas, it was An. arabiensis, with 36 ib/h, that played that role in Ambohitromby. Conclusions Despite a similar malaria prevalence in two nearby villages, the entomological survey showed a different contribution of An. coustani and An. arabiensis to malaria transmission in each village. Importantly, the suspected secondary malaria vector An. coustani, was found playing the major role in malaria transmission in one village. This highlights the importance of combining parasitology and entomology surveys for better targeting local malaria vectors. Such study should contribute to the malaria pre-elimination goal established under the 2018–2022 National Malaria Strategic Plan. ![]()
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Affiliation(s)
- Jessy Goupeyou-Youmsi
- Immunology of Infectious Diseases Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar. .,Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France. .,Doctoral School "Complexité du Vivant", Sorbonne University, Paris, France.
| | - Tsiriniaina Rakotondranaivo
- G4 Malaria Group, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Doctoral School "Génie du vivant et modélisation" Mahajanga University, Mahajanga, Madagascar
| | - Nicolas Puchot
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique UMR2000, Institut Pasteur, Paris, France
| | - Ingrid Peterson
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Romain Girod
- Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Inès Vigan-Womas
- Immunology of Infectious Diseases Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Richard Paul
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique UMR2000, Institut Pasteur, Paris, France
| | | | - Catherine Bourgouin
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France. .,Centre National de la Recherche Scientifique UMR2000, Institut Pasteur, Paris, France.
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39
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Goupeyou-Youmsi J, Rakotondranaivo T, Puchot N, Peterson I, Girod R, Vigan-Womas I, Paul R, Ndiath MO, Bourgouin C. Differential contribution of Anopheles coustani and Anopheles arabiensis to the transmission of Plasmodium falciparum and Plasmodium vivax in two neighbouring villages of Madagascar. Parasit Vectors 2020; 13:430. [PMID: 32843082 DOI: 10.1101/787432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 08/03/2020] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Malaria is still a heavy public health concern in Madagascar. Few studies combining parasitology and entomology have been conducted despite the need for accurate information to design effective vector control measures. In a Malagasy region of moderate to intense transmission of both Plasmodium falciparum and P. vivax, parasitology and entomology have been combined to survey malaria transmission in two nearby villages. METHODS Community-based surveys were conducted in the villages of Ambohitromby and Miarinarivo at three time points (T1, T2 and T3) during a single malaria transmission season. Human malaria prevalence was determined by rapid diagnostic tests (RDTs), microscopy and real-time PCR. Mosquitoes were collected by human landing catches and pyrethrum spray catches and the presence of Plasmodium sporozoites was assessed by TaqMan assay. RESULTS Malaria prevalence was not significantly different between villages, with an average of 8.0% by RDT, 4.8% by microscopy and 11.9% by PCR. This was mainly due to P. falciparum and to a lesser extent to P. vivax. However, there was a significantly higher prevalence rate as determined by PCR at T2 ([Formula: see text] = 7.46, P = 0.025). Likewise, mosquitoes were significantly more abundant at T2 ([Formula: see text] = 64.8, P < 0.001), especially in Ambohitromby. At T1 and T3 mosquito abundance was higher in Miarinarivo than in Ambohitromby ([Formula: see text] = 14.92, P < 0.001). Of 1550 Anopheles mosquitoes tested, 28 (1.8%) were found carrying Plasmodium sporozoites. The entomological inoculation rate revealed that Anopheles coustani played a major contribution in malaria transmission in Miarinarivo, being responsible of 61.2 infective bites per human (ib/h) during the whole six months of the survey, whereas, it was An. arabiensis, with 36 ib/h, that played that role in Ambohitromby. CONCLUSIONS Despite a similar malaria prevalence in two nearby villages, the entomological survey showed a different contribution of An. coustani and An. arabiensis to malaria transmission in each village. Importantly, the suspected secondary malaria vector An. coustani, was found playing the major role in malaria transmission in one village. This highlights the importance of combining parasitology and entomology surveys for better targeting local malaria vectors. Such study should contribute to the malaria pre-elimination goal established under the 2018-2022 National Malaria Strategic Plan.
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Affiliation(s)
- Jessy Goupeyou-Youmsi
- Immunology of Infectious Diseases Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France.
- Doctoral School "Complexité du Vivant", Sorbonne University, Paris, France.
| | - Tsiriniaina Rakotondranaivo
- G4 Malaria Group, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Doctoral School "Génie du vivant et modélisation" Mahajanga University, Mahajanga, Madagascar
| | - Nicolas Puchot
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique UMR2000, Institut Pasteur, Paris, France
| | - Ingrid Peterson
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Romain Girod
- Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Inès Vigan-Womas
- Immunology of Infectious Diseases Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Richard Paul
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique UMR2000, Institut Pasteur, Paris, France
| | | | - Catherine Bourgouin
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France.
- Centre National de la Recherche Scientifique UMR2000, Institut Pasteur, Paris, France.
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40
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Gupta E, Padhi A, Khodare A, Agarwal R, Ramachandran K, Mehta V, Kilikdar M, Dubey S, Kumar G, Sarin SK. Pooled RNA sample reverse transcriptase real time PCR assay for SARS CoV-2 infection: A reliable, faster and economical method. PLoS One 2020; 15:e0236859. [PMID: 32730368 PMCID: PMC7392263 DOI: 10.1371/journal.pone.0236859] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/15/2020] [Indexed: 12/24/2022] Open
Abstract
Background Corona virus disease 2019 (COVID-19) which initially started as a cluster of pneumonia cases in the Wuhan city of China has now become a full-blown pandemic. Timely diagnosis of COVID-19 is the key in containing the pandemic and breaking the chain of transmission. In low- and middle-income countries availability of testing kits has become the major bottleneck in testing. Novel methods like pooling of samples are the need of the hour. Objective We undertook this study to evaluate a novel protocol of pooling of RNA samples/elutes in performance of PCR for SARS CoV-2 virus. Study design Extracted RNA samples were randomly placed in pools of 8 on a 96 well plate. Both individual RNA (ID) and pooled RNA RT-qPCR for the screening E gene were done in the same plate and the positivity for the E gene was seen. Results The present study demonstrated that pool testing with RNA samples can easily detect even up to a single positive sample with Ct value as high as 38. The present study also showed that the results of pool testing is not affected by number of positive samples in a pool. Conclusion Pooling of RNA samples can reduce the time and expense, and can help expand diagnostic capabilities, especially during constrained supply of reagents and PCR kits for the diagnosis of SARS-CoV-2 infection.
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Affiliation(s)
- Ekta Gupta
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Abhishek Padhi
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Arvind Khodare
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Reshu Agarwal
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Krithiga Ramachandran
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Vibha Mehta
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Mousumi Kilikdar
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Shantanu Dubey
- Department of Hospital Operations, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Guresh Kumar
- Department of Clinical Research, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Shiv Kumar Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
- * E-mail:
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41
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Grossenbacher B, Holzschuh A, Hofmann NE, Omar KA, Stuck L, Fakih BS, Ali A, Yukich J, Hetzel MW, Felger I. Molecular methods for tracking residual Plasmodium falciparum transmission in a close-to-elimination setting in Zanzibar. Malar J 2020; 19:50. [PMID: 31996210 PMCID: PMC6988349 DOI: 10.1186/s12936-020-3127-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/16/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Molecular detection of low-density Plasmodium falciparum infections is essential for surveillance studies conducted to inform malaria control strategies in close-to-elimination settings. Molecular monitoring of residual malaria infections usually requires a large study size, therefore sampling and diagnostic processes need to be economical and optimized for high-throughput. A method comparison was undertaken to identify the most efficient diagnostic procedure for processing large collections of community samples with optimal test sensitivity, simplicity, and minimal costs. METHODS In a reactive case detection study conducted on Zanzibar, parasitaemia of 4590 individuals of all ages was investigated by a highly sensitive quantitative (q) PCR that targets multiple var gene copies per parasite genome. To reduce cost, a first round of positivity screening was performed on pools of dried blood spots from five individuals. Ten cycles of a pre-PCR were performed directly on the filter paper punches, followed by qPCR. In a second round, samples of positive pools were individually analysed by pre-PCR and qPCR. RESULTS Prevalence in household members and neighbors of index cases was 1.7% (78/4590) with a geometric mean parasite density of 58 parasites/µl blood. Using qPCR as gold standard, diagnostic sensitivity of rapid diagnostic tests (RDTs) was 37% (29/78). Infections positive by qPCR but negative by RDT had mean densities of 15 parasites/µl blood. CONCLUSION The approach of pre-screening reactive case detection samples in pools of five was ideal for a low prevalence setting such as in Zanzibar. Performing direct PCR on filter paper punches saves substantial time and justifies the higher cost for a polymerase suitable for amplifying DNA directly from whole blood. Molecular monitoring in community samples provided a more accurate picture of infection prevalence, as it identified a potential reservoir of infection that was largely missed by RDT. The developed qPCR-based methodology for screening large sample sets represents primarily a research tool that should inform the design of malaria elimination strategies. It may also prove beneficial for diagnostic tasks in surveillance-response activities.
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Affiliation(s)
- Benjamin Grossenbacher
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Aurel Holzschuh
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Natalie E Hofmann
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Kali Abdullah Omar
- Zanzibar Malaria Elimination Programme, Ministry of Health, Zanzibar, United Republic of Tanzania
| | - Logan Stuck
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, USA
| | | | - Abdullah Ali
- Zanzibar Malaria Elimination Programme, Ministry of Health, Zanzibar, United Republic of Tanzania
| | - Joshua Yukich
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, USA
| | - Manuel W Hetzel
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
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42
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Balasubramanian S, Rahman RS, Lon C, Parobek C, Ubalee R, Hathaway N, Kuntawunginn W, My M, Vy D, Saxe J, Lanteri C, Lin FC, Spring M, Meshnick SR, Juliano JJ, Saunders DL, Lin JT. Efficient Transmission of Mixed Plasmodium falciparum/vivax Infections From Humans to Mosquitoes. J Infect Dis 2020; 221:428-437. [PMID: 31549156 PMCID: PMC7184918 DOI: 10.1093/infdis/jiz388] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/23/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND In Southeast Asia, people are often coinfected with different species of malaria (Plasmodium falciparum [Pf] and Plasmodium vivax [Pv]) as well as with multiple clones of the same species. Whether particular species or clones within mixed infections are more readily transmitted to mosquitoes remains unknown. METHODS Laboratory-reared Anopheles dirus were fed on blood from 119 Pf-infected Cambodian adults, with 5950 dissected to evaluate for transmitted infection. Among 12 persons who infected mosquitoes, polymerase chain reaction and amplicon deep sequencing were used to track species and clone-specific transmission to mosquitoes. RESULTS Seven of 12 persons that infected mosquitoes harbored mixed Pf/Pv infection. Among these 7 persons, all transmitted Pv with 2 transmitting both Pf and Pv, leading to Pf/Pv coinfection in 21% of infected mosquitoes. Up to 4 clones of each species were detected within persons. Shifts in clone frequency were detected during transmission. However, in general, all parasite clones in humans were transmitted to mosquitoes, with individual mosquitoes frequently carrying multiple transmitted clones. CONCLUSIONS Malaria diversity in human hosts was maintained in the parasite populations recovered from mosquitoes fed on their blood. However, in persons with mixed Pf/Pv malaria, Pv appears to be transmitted more readily, in association with more prevalent patent gametocytemia.
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Affiliation(s)
- Sujata Balasubramanian
- Institute of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill
| | - Rifat S Rahman
- Institute of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill
| | - Chanthap Lon
- Armed Forces Research Institute of Medical Sciences, Phnom Penh, Cambodia
| | - Christian Parobek
- Institute of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill
| | - Ratawan Ubalee
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Nicholas Hathaway
- Department of Bioinformatics and Integrated Biology, University of Massachusetts, Worcester
| | - Worachet Kuntawunginn
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mok My
- Royal Cambodian Armed Forces, Phnom Penh, Cambodia
| | - Dav Vy
- Royal Cambodian Armed Forces, Phnom Penh, Cambodia
| | - Jeremy Saxe
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill
| | - Charlotte Lanteri
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Feng-Chang Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill
| | - Michele Spring
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill
| | - Jonathan J Juliano
- Institute of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill
| | - David L Saunders
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- US Army Medical Materiel Development Activity, Fort Detrick, Maryland
| | - Jessica T Lin
- Institute of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill
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Deutsch-Feldman M, Aydemir O, Carrel M, Brazeau NF, Bhatt S, Bailey JA, Kashamuka M, Tshefu AK, Taylor SM, Juliano JJ, Meshnick SR, Verity R. The changing landscape of Plasmodium falciparum drug resistance in the Democratic Republic of Congo. BMC Infect Dis 2019; 19:872. [PMID: 31640574 PMCID: PMC6805465 DOI: 10.1186/s12879-019-4523-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Drug resistant malaria is a growing concern in the Democratic Republic of the Congo (DRC), where previous studies indicate that parasites resistant to sulfadoxine/pyrimethamine or chloroquine are spatially clustered. This study explores longitudinal changes in spatial patterns to understand how resistant malaria may be spreading within the DRC, using samples from nation-wide population-representative surveys. METHODS We selected 552 children with PCR-detectable Plasmodium falciparum infection and identified known variants in the pfdhps and pfcrt genes associated with resistance. We compared the proportion of mutant parasites in 2013 to those previously reported from adults in 2007, and identified risk factors for carrying a resistant allele using multivariate mixed-effects modeling. Finally, we fit a spatial-temporal model to the observed data, providing smooth allele frequency estimates over space and time. RESULTS The proportion of co-occurring pfdhps K540E/A581G mutations increased by 16% between 2007 and 2013. The spatial-temporal model suggests that the spatial range of the pfdhps double mutants expanded over time, while the prevalence and range of pfcrt mutations remained steady. CONCLUSIONS This study uses population-representative samples to describe the changing landscape of SP resistance within the DRC, and the persistence of chloroquine resistance. Vigilant molecular surveillance is critical for controlling the spread of resistance.
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Affiliation(s)
- Molly Deutsch-Feldman
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA.
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Margaret Carrel
- Department of Geographical & Sustainability Sciences, University of Iowa, Iowa City, IA, USA
| | - Nicholas F Brazeau
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
| | - Samir Bhatt
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Melchior Kashamuka
- Ecole de Santé Publique, , Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Antoinette K Tshefu
- Ecole de Santé Publique, , Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Steve M Taylor
- Division of Infectious Diseases and Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA.,Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
| | - Robert Verity
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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44
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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: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [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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Geographical heterogeneity in prevalence of subclinical malaria infections at sentinel endemic sites of Myanmar. Parasit Vectors 2019; 12:83. [PMID: 30777127 PMCID: PMC6378722 DOI: 10.1186/s13071-019-3330-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/31/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The malaria burden of Myanmar still remains high within the Greater Mekong Subregion of Southeast Asia. An important indicator of progress towards malaria elimination is the prevalence of parasite infections in endemic populations. Information about malaria epidemiology is mostly derived from reports of confirmed acute malaria cases through passive case detection, whereas the prevalence of baseline subclinical malaria infections is much less known. METHODS In this study, cross-sectional surveys were conducted during the rainy season of 2017 in four townships (Bilin, Thabeikkyin, Banmauk and Paletwa) of Myanmar with divergent annual malaria incidences. A total of 1991 volunteers were recruited from local villages and Plasmodium subclinical infections were estimated by light microscopy (LM), rapid diagnostic tests (RDTs) and nested PCR. The nested PCR analysis was performed with a modified pooling strategy that was optimized based on an initial estimate the infection prevalence. RESULTS The overall malaria infection prevalence based on all methods was 13.9% (277/1991) and it differed drastically among the townships, with Paletwa in the western border having the highest infection rate (22.9%) and Thabeikkyin in central Myanmar having the lowest (3.9%). As expected, nested PCR was the most sensitive and identified 226 (11.4%) individuals with parasite infections. Among the parasite species, Plasmodium vivax was the most prevalent in all locations, while Plasmodium falciparum also accounted for 32% of infections in the western township Paletwa. Two RDTs based on the detection of the hrp2 antigen detected a total of 103 P. falciparum infections, and the ultrasensitive RDT detected 20% more P. falciparum infections than the conventional RDT. In contrast, LM missed the majority of the subclinical infections and only identified 14 Plasmodium infections. CONCLUSIONS Cross-sectional surveys identified considerable levels of asymptomatic Plasmodium infections in endemic populations of Myanmar with P. vivax becoming the predominant parasite species. Geographical heterogeneity of subclinical infections calls for active surveillance of parasite infections in endemic areas. The pooling scheme designed for nested PCR analysis offers a more practical strategy for large-scale epidemiological studies of parasite prevalence. Such information is important for decision-makers to put forward a more realistic action plan for malaria elimination.
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Boyce RM, Hathaway N, Fulton T, Reyes R, Matte M, Ntaro M, Mulogo E, Waltmann A, Bailey JA, Siedner MJ, Juliano JJ. Reuse of malaria rapid diagnostic tests for amplicon deep sequencing to estimate Plasmodium falciparum transmission intensity in western Uganda. Sci Rep 2018; 8:10159. [PMID: 29977002 PMCID: PMC6033881 DOI: 10.1038/s41598-018-28534-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/25/2018] [Indexed: 01/29/2023] Open
Abstract
Molecular techniques are not routinely employed for malaria surveillance, while cross-sectional, community-based parasite surveys require significant resources. Here, we describe a novel use of malaria rapid diagnostic tests (RDTs) collected at a single facility as source material for sequencing to esimtate malaria transmission intensity across a relatively large catchment area. We extracted Plasmodium falciparum DNA from RDTs, then amplified and sequenced a region of the apical membrane antigen 1 (pfama1) using targeted amplicon deep sequencing. We determined the multiplicity of infection (MOI) for each sample and examined associations with demographic, clinical, and spatial factors. We successfully genotyped 223 of 287 (77.7%) of the samples. We demonstrated an inverse relationship between the MOI and elevation with individuals presenting from the highest elevation villages harboring infections approximately half as complex as those from the lowest (MOI 1.85 vs. 3.51, AOR 0.25, 95% CI 0.09-0.65, p = 0.004). This study demonstrates the feasibility and validity of using routinely-collected RDTs for molecular surveillance of malaria and has real-world utility, especially as the cost of high-throughpout sequencing continues to decline.
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Affiliation(s)
- Ross M Boyce
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA.
| | - Nick Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, 368 Plantation St., Worcester, Massachusetts, 01605, USA
| | - Travis Fulton
- Division of Epidemiology, University of North Carolina at Chapel Hill Gillings School of Global Public Health, 135 Dauer Drive, Chapel Hill, 27599, USA
| | - Raquel Reyes
- Division of General Medicine & Clinical Epidemiology, University of North Carolina at Chapel Hill, 5039 Old Clinic Building, CB 7110, Chapel Hill, 27599, USA
| | - Michael Matte
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Moses Ntaro
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Edgar Mulogo
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Andreea Waltmann
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, 368 Plantation St., Worcester, Massachusetts, 01605, USA
| | - Mark J Siedner
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, 125 Nashua Street, Suite 722, Boston, 02114, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA.,Division of Epidemiology, University of North Carolina at Chapel Hill Gillings School of Global Public Health, 135 Dauer Drive, Chapel Hill, 27599, USA.,Curriculum in Genetics and Microbiology, University of North Carolina at Chapel Hill, 321 South Columbia Street, Chapel Hill, NC, 27516, USA
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Markwalter CF, Gibson LE, Mudenda L, Kimmel DW, Mbambara S, Thuma PE, Wright DW. Characterization of Plasmodium Lactate Dehydrogenase and Histidine-Rich Protein 2 Clearance Patterns via Rapid On-Bead Detection from a Single Dried Blood Spot. Am J Trop Med Hyg 2018; 98:1389-1396. [PMID: 29557342 PMCID: PMC5953395 DOI: 10.4269/ajtmh.17-0996] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A rapid, on-bead enzyme-linked immunosorbent assay for Plasmodium lactate dehydrogenase (pLDH) and Plasmodium falciparum histidine-rich protein 2 (HRP2) was adapted for use with dried blood spot (DBS) samples. This assay detected both biomarkers from a single DBS sample with only 45 minutes of total incubation time and detection limits of 600 ± 500 pM (pLDH) and 69 ± 30 pM (HRP2), corresponding to 150 and 24 parasites/μL, respectively. This sensitive and reproducible on-bead detection method was used to quantify pLDH and HRP2 in patient DBS samples from rural Zambia collected at multiple time points after treatment. Biomarker clearance patterns relative to parasite clearance were determined; pLDH clearance followed closely with parasite clearance, whereas most patients maintained detectable levels of HRP2 for 35–52 days after treatment. Furthermore, weak-to-moderate correlations between biomarker concentration and parasite densities were found for both biomarkers. This work demonstrates the utility of the developed assay for epidemiological study and surveillance of malaria.
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Affiliation(s)
| | - Lauren E Gibson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Lwiindi Mudenda
- Rusangu University, Monze, Zambia.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Danielle W Kimmel
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | | | | | - David W Wright
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
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48
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Verity R, Hathaway NJ, Waltmann A, Doctor SM, Watson OJ, Patel JC, Mwandagalirwa K, Tshefu AK, Bailey JA, Ghani AC, Juliano JJ, Meshnick SR. Plasmodium falciparum genetic variation of var2csa in the Democratic Republic of the Congo. Malar J 2018; 17:46. [PMID: 29361940 PMCID: PMC5782373 DOI: 10.1186/s12936-018-2193-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Democratic Republic of the Congo (DRC) bears a high burden of malaria, which is exacerbated in pregnant women. The VAR2CSA protein plays a crucial role in pregnancy-associated malaria (PAM), and hence quantifying diversity at the var2csa locus in the DRC is important in understanding the basic epidemiology of PAM, and in developing a robust vaccine against PAM. METHODS Samples were taken from the 2013-14 Demographic and Health Survey conducted in the DRC, focusing on children under 5 years of age. A short subregion of the var2csa gene was sequenced in 115 spatial clusters, giving country-wide estimates of sequence polymorphism and spatial population structure. RESULTS Results indicate that var2csa is highly polymorphic, and that diversity is being maintained through balancing selection, however, there is no clear signal of phylogenetic or geographic structure to this diversity. Linear modelling demonstrates that the number of var2csa variants in a cluster correlates directly with cluster prevalence, but not with other epidemiological factors such as urbanicity. CONCLUSIONS Results suggest that the DRC fits within the global pattern of high var2csa diversity and little genetic differentiation between regions. A broad multivalent VAR2CSA vaccine candidate could benefit from targeting stable regions and common variants to address the substantial genetic diversity.
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Affiliation(s)
- Robert Verity
- Medical Research Council Centre for Outbreak Analysis & Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Nicholas J Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester, MA, USA
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts, Worcester, MA, USA
| | - Andreea Waltmann
- Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Stephanie M Doctor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Oliver J Watson
- Medical Research Council Centre for Outbreak Analysis & Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jaymin C Patel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Kashamuka Mwandagalirwa
- Kinshasa School of Public Health, Hôpital General Provincial de Reference de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Antoinette K Tshefu
- Community Health, Kinshasa School of Public Health, School of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester, MA, USA
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts, Worcester, MA, USA
| | - Azra C Ghani
- Medical Research Council Centre for Outbreak Analysis & Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, USA
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA
- Curriculum in Genetics and Microbiology, University of North Carolina at Chapel Hill, 321 South Columbia Street, Chapel Hill, NC, 27516, USA
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, USA
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49
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Mester P, Witte AK, Robben C, Streit E, Fister S, Schoder D, Rossmanith P. Optimization and evaluation of the qPCR-based pooling strategy DEP-pooling in dairy production for the detection of Listeria monocytogenes. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.06.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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50
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Bakr S, Edris S, Abdel Fattah NS, Ibrahim NM, El-Khadragy MF. Molecular Screening for Malaria among Blood Donors in a WHO Claimed Region of Egypt, Fayoum Governorate. Mediterr J Hematol Infect Dis 2017; 9:e2017065. [PMID: 29181142 PMCID: PMC5667524 DOI: 10.4084/mjhid.2017.065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 09/25/2017] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Transfusion-transmitted malaria is undoubtedly a potential health hazard for blood recipients. Egypt is still on the prevention of reintroduction phase of malaria control program. Fayoum Governorate is considered one of the high-risk foci in Egypt due to its geology. However, no studies have been reported to evaluate the current status of subclinical Plasmodium infection based on sensitive molecular techniques. Moreover, screening of malaria is not listed within screening protocols of blood-borne pathogens in Fayoum blood banks. OBJECTIVE To assess the current prevalence of subclinical Plasmodium infection among blood donors of Fayoum inhabitants for transfusion biosafety. To predict any possibility of the reemergence of malaria in the governorate and the effectiveness of malaria control measures. METHODS A cross-sectional survey was conducted on 400 apparently healthy blood-donors in blood transfusion center of Fayoum University hospital from Jun 2012 to Jan 2013. Conventional PCR was used to detect the 18 S ssrRNA Plasmodium gene. RESULTS All Fayoum inhabitants' blood donors' samples were negative for Plasmodium infection. CONCLUSIONS Current applied control, and preventive measures are valid in the context of blood transfusion biosafety in Fayoum blood banks and, therefore, the implementation of a routine malaria screening test in Fayoum blood banks is not merited at this time.
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Affiliation(s)
- Salwa Bakr
- Department of Clinical Pathology, College of Medicine, Fayoum University, Fayoum, Egypt
- College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudia Arabia
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | | | | | - Manal F. El-Khadragy
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Chair Vaccines Research of Infectious Diseases, Faculty of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Zoology and Entomology, Faculty of Science, Helwan University, Cairo, Egypt
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