Need for additional capacity and improved capability for molecular detection of yellow fever virus in European Expert Laboratories: External Quality Assessment, March 2018

Excellent capability for molecular detection of Aedes-borne dengue, Zika, and chikungunya viruses but with a need for increased capacity for yellow fever and Japanese encephalitis viruses: an external quality assessment in 36 European laboratories

Mosquito-borne viruses represent a large global health burden. With geographic expansion of competent vectors for chikungunya virus (CHIKV), dengue virus (DENV), and Zika virus (ZIKV) in Europe, it is anticipated that the number of autochthonous cases of these tropical viruses in Europe will increase. Therefore, regular assessment of diagnostic capabilities in Europe is important. Our aim was to evaluate the mosquito-borne virus molecular detection capability of expert European laboratories by conducting an external quality assessment in October 2023. Molecular panels included 12 plasma samples: one alphavirus (CHIKV), four orthoflaviviruses (ZIKV, yellow fever virus [YFV], DENV, and Japanese encephalitis virus [JEV]), and two negative control samples. Mosquito-borne virus detection was assessed among 36 laboratories in 24 European countries. Adequate capabilities were lacking for YFV and JEV. Many laboratories relied on a mix of laboratory-developed tests (some of which were pan-orthoflavivirus or pan-alphavirus in combination with sequencing) and commercial assays. 47.2% of laboratories characterized all external quality assessment (EQA) samples correctly. Correct result rates were 100% for CHIKV and ZIKV and >99% for DENV, but laboratories lacked capacity, specificity, and sensitivity for JEV and YFV. Three of the viruses in this panel emerged and transiently circulated in Europe: CHIKV, ZIKV, and DENV. Molecular detection was excellent for those viruses, but <50% is accurate for the remainder of the panel. With the possibility or continuation of imported cases and a growing global concern about climate change and vector expansion, progress toward rapid, accurate mosquito-borne virus diagnostics in Europe is recommended, as well as regular EQAs to monitor it.IMPORTANCEThe external quality assessment (EQA) focused on Aedes-borne viruses: chikungunya virus (CHIKV), dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV). Japanese encephalitis virus, an orthoflavivirus that is spread by mosquito species belonging to the genus Culex, was included in the quality assessment as well. CHIKV, DENV, and ZIKV have proven potential for transient and limited circulation in Europe upon introduction of viremic travelers returning to Aedes albopictus-endemic regions. Results of this EQA were excellent for those viruses, but <50% is accurate for the remainder of the panel (YFV and Japanese encephalitis virus). Considering imported cases and the threat of climate change and competent vector expansion, progress toward rapid, accurate mosquito-borne virus diagnostics in Europe is recommended.

Laboratory capacity assessments in 25 African countries at high risk of yellow fever, August-December 2018

INTRODUCTION

accurate and timely laboratory diagnosis of yellow fever (YF) is critical to the Eliminate Yellow Fever Epidemics (EYE) strategy. Gavi, the Vaccine Alliance recognized the need to support and build capacity in the national and regional laboratories in the Global YF Laboratory Network (GYFLN) as part of this strategy.

METHODS

to better understand current capacity, gaps and needs of the GYFLN laboratories in Africa, assessments were carried out in national and regional reference laboratories in the 25 African countries at high risk for YF outbreaks that were eligible for new financial support from Gavi.

RESULTS

the assessments found that the GYFLN in Africa has high capacity but 21% of specimens were not tested due to lack of testing kits or reagents and approximately 50% of presumptive YF cases were not confirmed at the regional reference laboratory due to problems with shipping.

CONCLUSION

the laboratory assessments helped to document the baseline capacities of these laboratories prior to Gavi funding to support strengthening YF laboratories.

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Background

The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur.

Aim

We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available.

Methods

Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology.

Results

The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive – Global (EVAg), a European Union infrastructure project.

Conclusion

The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

Yellow fever control: current epidemiology and vaccination strategies

Yellow fever (YF) outbreaks continue, have expanded into new areas and threaten large populations in South America and Africa. Predicting where epidemics might occur must take into account local mosquito populations and specific YF virus strain, as well as ecoclimatic conditions, sociopolitical and demographic factors including population size, density, and mobility, and vaccine coverage. Populations of Aedes aegypti and Aedes albopictus from different regions vary in susceptibility to and capacity to transmit YF virus. YF virus cannot be eliminated today because the virus circulates in animal reservoirs, but human disease could be eliminated with wide use of the vaccine. WHO EYE (Eliminate Yellow Fever Epidemics) is a welcome plan to control YF, with strategies to be carried out from 2017 to 2026: to expand use of YF vaccine, to prevent international spread, and to contain outbreaks rapidly. YF vaccination is the mainstay in controlling YF outbreaks, but global supply is insufficient. Therefore, dose-sparing strategies have been proposed including fractional dosing and intradermal administration. Fractional dosing has been effectively used in outbreak control but currently does not satisfy International Health Regulations; special documentation is needed for international travel. Vector control is another facet in preventing YF outbreaks, and novel methods are being considered and proposed.

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

BACKGROUND

The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur.

AIM

We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available.

METHODS

Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology.

RESULTS

The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive - Global (EVAg), a European Union infrastructure project.

CONCLUSION

The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

BACKGROUND

The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur.

AIM

We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available.

METHODS

Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology.

RESULTS

The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive - Global (EVAg), a European Union infrastructure project.

CONCLUSION

The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

BACKGROUND

The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur.

AIM

We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available.

METHODS

Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology.

RESULTS

The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive - Global (EVAg), a European Union infrastructure project.

CONCLUSION

The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

BACKGROUND

The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur.

AIM

We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available.

METHODS

Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology.

RESULTS

The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive - Global (EVAg), a European Union infrastructure project.

CONCLUSION

The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

What Does the Future Hold for Yellow Fever Virus? (II)

As revealed by the recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America, YFV control measures need urgent rethinking. Over the last decade, most reported outbreaks occurred in, or eventually reached, areas with low vaccination coverage but that are suitable for virus transmission, with an unprecedented risk of expansion to densely populated territories in Africa, South America and Asia. As reflected in the World Health Organization's initiative launched in 2017, it is high time to strengthen epidemiological surveillance to monitor accurately viral dissemination, and redefine vaccination recommendation areas. Vector-control and immunisation measures need to be adapted and vaccine manufacturing must be reconciled with an increasing demand. We will have to face more yellow fever (YF) cases in the upcoming years. Hence, improving disease management through the development of efficient treatments will prove most beneficial. Undoubtedly, these developments will require in-depth descriptions of YFV biology at molecular, physiological and ecological levels. This second section of a two-part review describes the current state of knowledge and gaps regarding the molecular biology of YFV, along with an overview of the tools that can be used to manage the disease at the individual, local and global levels.