Macroarray assay for differential diagnosis of meningoencephalitis in southern Africa

Venter, Marietjie; Zaayman, Dewald; Niekerk, Stephanie van; Stivaktas, Voula; Goolab, Shivani; Weyer, Jacqueline; Pawęska, Janusz T.; Swanepoel, Robert

doi:10.1016/j.jcv.2014.02.001

Cited by 19 publications

(19 citation statements)

References 23 publications

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“…Among AFDUC patients, a multiplex PCR-based macroarray assay ( Fever Chip ) will be used on whole blood and CSF specimens for differential diagnosis of 30 pathogens associated with febrile disease, haemorrhagic fever disease and meningo-encephalitis including both common and less frequently encountered viruses, bacteria, parasites, and arboviruses of medical importance in SSA [ 30 ]. Pathogens included on the Fever Chip are Crimean-Congo haemorrhagic fever virus, Rift Valley Fever virus, West Nile virus, Chikungunya virus, Dengue virus, Sindbis virus, Rubella virus, Cytomegalovirus, Measles virus, Mumps virus, Herpes simplex 1 and 2 viruses, Varicella Zoster virus, Rabies virus, Epstein-Barr virus, JC virus, Enterovirus, Adenovirus, Flavivirus family, Hepatitis A and B viruses, Rickettsia spp., Borrelia burgdorferi / garinii , Brucella spp., Coxiella burnetti , Leptospira spp.…”

Section: Methods and Settingmentioning

confidence: 99%

The African Network for Improved Diagnostics, Epidemiology and Management of common infectious Agents

et al. 2021

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Background In sub-Saharan Africa, acute respiratory infections (ARI), acute gastrointestinal infections (GI) and acute febrile disease of unknown cause (AFDUC) have a large disease burden, especially among children, while respective aetiologies often remain unresolved. The need for robust infectious disease surveillance to detect emerging pathogens along with common human pathogens has been highlighted by the ongoing novel coronavirus disease 2019 (COVID-19) pandemic. The African Network for Improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA) is a sentinel surveillance study on the aetiology and clinical characteristics of ARI, GI and AFDUC in sub-Saharan Africa. Methods ANDEMIA includes 12 urban and rural health care facilities in four African countries (Côte d’Ivoire, Burkina Faso, Democratic Republic of the Congo and Republic of South Africa). It was piloted in 2018 in Côte d’Ivoire and the initial phase will run from 2019 to 2021. Case definitions for ARI, GI and AFDUC were established, as well as syndrome-specific sampling algorithms including the collection of blood, naso- and oropharyngeal swabs and stool. Samples are tested using comprehensive diagnostic protocols, ranging from classic bacteriology and antimicrobial resistance screening to multiplex real-time polymerase chain reaction (PCR) systems and High Throughput Sequencing. In March 2020, PCR testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and analysis of full genomic information was included in the study. Standardised questionnaires collect relevant clinical, demographic, socio-economic and behavioural data for epidemiologic analyses. Controls are enrolled over a 12-month period for a nested case-control study. Data will be assessed descriptively and aetiologies will be evaluated using a latent class analysis among cases. Among cases and controls, an integrated analytic approach using logistic regression and Bayesian estimation will be employed to improve the assessment of aetiology and associated risk factors. Discussion ANDEMIA aims to expand our understanding of ARI, GI and AFDUC aetiologies in sub-Saharan Africa using a comprehensive laboratory diagnostics strategy. It will foster early detection of emerging threats and continued monitoring of important common pathogens. The network collaboration will be strengthened and site diagnostic capacities will be reinforced to improve quality management and patient care.

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Section: Methods and Settingmentioning

confidence: 99%

The African Network for Improved Diagnostics, Epidemiology and Management of common infectious Agents

et al. 2021

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“…A multiplex PCR-based macroarray assay (Chipron, GmBH), developed and validated at the Emerging vector-borne and respiratory virus program, Centre for Viral Zoonoses, University of Pretoria, South Africa, was used for simultaneous detection of 30 pathogens ( S1 Table ). The methods previously described[ 26 ] combined conventional multiplex PCR with hybridization of biotinylated PCR products to streptavidin labeled probes on a macroarray chip (Chipron GmBH), followed by colorimetric detection. Briefly, each specimen is subjected to 2 multiplex PCR reactions containing biotinylated primers targeted to the 30 pathogens.…”

Section: Methodsmentioning

confidence: 99%

Study on causes of fever in primary healthcare center uncovers pathogens of public health concern in Madagascar

Guillebaud

Bernardson

Randriambolamanantsoa

et al. 2018

PLoS Negl Trop Dis

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BackgroundThe increasing use of malaria diagnostic tests reveals a growing proportion of patients with fever but no malaria. Clinicians and health care workers in low-income countries have few tests to diagnose causes of fever other than malaria although several diseases share common symptoms. We propose here to assess etiologies of fever in Madagascar to ultimately improve management of febrile cases.MethodologyConsenting febrile outpatients aged 6 months and older were recruited in 21 selected sentinel sites throughout Madagascar from April 2014 to September 2015. Standard clinical examinations were performed, and blood and upper respiratory specimens were taken for rapid diagnostic tests and molecular assays for 36 pathogens of interest for Madagascar in terms of public health, regardless of clinical status.Principal findingsA total of 682 febrile patients were enrolled. We detected at least one pathogen in 40.5% (276/682) of patients and 6.2% (42/682) with co-infections. Among all tested patients, 26.5% (181/682) had at least one viral infection, 17.0% (116/682) had malaria and 1.0% (7/682) presented a bacterial or a mycobacterial infection. None or very few of the highly prevalent infectious agents in Eastern Africa and Asia were detected in this study, such as zoonotic bacteria or arboviral infections.ConclusionsThese results raise questions about etiologies of fever in Malagasy communities. Nevertheless, we noted that viral infections and malaria still represent a significant proportion of causes of febrile illnesses. Interestingly our study allowed the detection of pathogens of public health interest such as Rift Valley Fever Virus but also the first case of laboratory-confirmed leptospirosis infection in Madagascar.

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“…However, a faster and safer diagnosis can be achieved through molecular methods using real‐time reverse transcriptase (RT)‐polymerase chain reaction (PCR) to detect viral RNA (OIE, ) thus minimisng the handling of infectious viruses. Different highly sensitive molecular tests have been developed for RVFV including nested RT‐PCR methods (Sall et al., ), quantitative real‐time PCR (Garcia et al., ; Drosten et al., ; Bird et al., ; Wilson et al., ), multiplex PCR‐based microarray assay (Venter et al., ), RT Loop‐mediated isothermal amplification (RT‐LAMP) (Le Roux et al., ) and recombinase polymerase amplification (RPA) (Euler et al., ). Molecular assays have also been used for the early detection of RVFV RNA in mosquito pools during surveillance activities (Jupp et al., ; LaBeaud et al., ).…”

Section: Assessmentmentioning

confidence: 99%

Rift Valley Fever – epidemiological update and risk of introduction into Europe

Nielsen¹,

Álvarez²,

Bicout³

et al. 2020

EFS2

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Rift Valley fever (RVF) is a vector‐borne disease transmitted by a broad spectrum of mosquito species, especially Aedes and Culex genus, to animals (domestic and wild ruminants and camels) and humans. Rift Valley fever is endemic in sub‐Saharan Africa and in the Arabian Peninsula, with periodic epidemics characterised by 5–15 years of inter‐epizootic periods. In the last two decades, RVF was notified in new African regions (e.g. Sahel), RVF epidemics occurred more frequently and low‐level enzootic virus circulation has been demonstrated in livestock in various areas. Recent outbreaks in a French overseas department and some seropositive cases detected in Turkey, Tunisia and Libya raised the attention of the EU for a possible incursion into neighbouring countries. The movement of live animals is the most important pathway for RVF spread from the African endemic areas to North Africa and the Middle East. The movement of infected animals and infected vectors when shipped by flights, containers or road transport is considered as other plausible pathways of introduction into Europe. The overall risk of introduction of RVF into EU through the movement of infected animals is very low in all the EU regions and in all MSs (less than one epidemic every 500 years), given the strict EU animal import policy. The same level of risk of introduction in all the EU regions was estimated also considering the movement of infected vectors, with the highest level for Belgium, Greece, Malta, the Netherlands (one epidemic every 228–700 years), mainly linked to the number of connections by air and sea transports with African RVF infected countries. Although the EU territory does not seem to be directly exposed to an imminent risk of RVFV introduction, the risk of further spread into countries neighbouring the EU and the risks of possible introduction of infected vectors, suggest that EU authorities need to strengthen their surveillance and response capacities, as well as the collaboration with North African and Middle Eastern countries.

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Macroarray assay for differential diagnosis of meningoencephalitis in southern Africa

Cited by 19 publications

References 23 publications

The African Network for Improved Diagnostics, Epidemiology and Management of common infectious Agents

The African Network for Improved Diagnostics, Epidemiology and Management of common infectious Agents

Study on causes of fever in primary healthcare center uncovers pathogens of public health concern in Madagascar

Rift Valley Fever – epidemiological update and risk of introduction into Europe

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