Re-Emergence of Dengue Serotype 3 in the Context of a Large Religious Gathering Event in Touba, Senegal

Existing operational standards for field deployments of rapid response mobile laboratories: a scoping review

Introduction

Rapid response mobile laboratories (RRML) play an important role in responding to emergencies such as outbreaks and humanitarian crises, working in coordination with national authorities. This scoping review aims to provide evidence to support the development of minimum operational standards for the deployment of RRMLs across the five key workstreams: operational support and logistics, biosafety and biosecurity, laboratory information management system, quality management systems and interoperability and coordination.

Methods

We searched PubMed, MEDLINE, EMBASE and the grey literature focusing on RRML deployment missions. Study characteristics such as year, country, objectives, methods, and findings were extracted and summarized to identify common themes, gaps, and patterns. The results were presented in a narrative format. We ensured methodological rigor by following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guidelines throughout the review process.

Results

Out of 163 full-text studies assessed for eligibility, 46 met the inclusion criteria and were analyzed. Six studies addressed the five RRML workstreams. Operational support and logistics are most commonly addressed during pre-deployment phases with a focus on personnel, transport and cold chain management. The application of biosafety and biosecurity protocols is most addressed during the mission execution phase, particularly in the use of personal protective equipment and the implementation of decontamination and disinfection procedures. The laboratory information management system procedures most frequently reported include sample identification and result dissemination protocols. The quality management system workstream overlaps significantly with the other four workstreams, with a strong emphasis on internal and external quality assurance measures. Coordination and interoperability aspects involve maintaining multiple collaborations, ranging from coordinating with local authorities to establishing international partnerships. Common field challenges included interrupted data transfer in areas characterized by poor connectivity and difficulties caused by extreme weather conditions.

Discussion

This review highlights RRML deployment procedures and addresses some critical challenges concerning their deployment. It suggests the provision of a pre-deployment logistics checklist, the use of a pre-determined standardized dataset for inputs to reduce data entry errors and the application of standardized internal and external quality assurance measures.

The Spatiotemporal Distribution and Molecular Characterization of Circulating Dengue Virus Serotypes/Genotypes in Senegal from 2019 to 2023

Dengue virus is becoming a major public health threat worldwide, principally in Africa. From 2016 to 2020, 23 outbreaks were reported in Africa, principally in West Africa. In Senegal, dengue outbreaks have been reported yearly since 2017. Data about the circulating serotypes and their spatial and temporal distribution were limited to outbreaks that occurred between 2017 and 2018. Herein, we describe up-to-date molecular surveillance of circulating DENV serotypes in Senegal between 2019 to 2023 and their temporal and spatial distribution around the country. For this purpose, suspected DENV-positive samples were collected and subjected to dengue detection and serotyping using RT-qPCR methods. Positive samples were used for temporal and spatial mapping. A subset of DENV+ samples were then sequenced and subjected to phylogenetic analysis. Results show a co-circulation of three DENV serotypes with an overall predominance of DENV-3. In terms of abundance, DENV-3 is followed by DENV-1, with scarce cases of DENV-2 from February 2019 to February 2022. Interestingly, data show the extinction of both serotype 1 and serotype 2 and the only circulation of DENV-3 from March 2022 to February 2023. At the genotype level, the analysis shows that sequenced strains belong to same genotype as previously described: Senegalese DENV-1 strains belong to genotype V, DENV-2 strains to the cosmopolitan genotype, and DENV-3 strains to Genotype III. Interestingly, newly obtained DENV 1-3 sequences clustered in different clades within genotypes. This co-circulation of strains belonging to different clades could have an effect on virus epidemiology and transmission dynamics. Overall, our results highlight DENV serotype replacement by DENV-3, accompanied by a wider geographic distribution, in Senegal. These results highlight the importance of virus genomic surveillance and call for further viral fitness studies using both in vitro and in vivo models, as well as in-depth phylogeographic studies to uncover the virus dispersal patterns across the country.

Molecular Evolution of Dengue Virus 3 in Senegal between 2009 and 2022: Dispersal Patterns and Implications for Prevention and Therapeutic Countermeasures

Dengue fever is the most prevalent arboviral disease worldwide. Dengue virus (DENV), the etiological agent, is known to have been circulating in Senegal since 1970, though for a long time, virus epidemiology was restricted to the circulation of sylvatic DENV-2 in south-eastern Senegal (the Kedougou region). In 2009 a major shift was noticed with the first urban epidemic, which occurred in the Dakar region and was caused by DENV-3. Following the notification by Senegal, many other West African countries reported DENV-3 epidemics. Despite these notifications, there are scarce studies and data about the genetic diversity and molecular evolution of DENV-3 in West Africa. Using nanopore sequencing, phylogenetic, and phylogeographic approaches on historic strains and 36 newly sequenced strains, we studied the molecular evolution of DENV-3 in Senegal between 2009 and 2022. We then assessed the impact of the observed genetic diversity on the efficacy of preventive countermeasures and vaccination by mapping amino acid changes against vaccine strains. The results showed that the DENV-3 strains circulating in Senegal belong to genotype III, similarly to strains from other West African countries, while belonging to different clades. Phylogeographic analysis based on nearly complete genomes revealed three independent introduction events from Asia and Burkina Faso. Comparison of the amino acids in the CprM-E regions of genomes from the Senegalese strains against the vaccine strains revealed the presence of 22 substitutions (7 within the PrM and 15 within the E gene) when compared to CYD-3, while 23 changes were observed when compared to TV003 (6 within the PrM and 17 within the E gene). Within the E gene, most of the changes compared to the vaccine strains were located in the ED-III domain, which is known to be crucial in neutralizing antibody production. Altogether, these data give up-to-date insight into DENV-3 genomic evolution in Senegal which needs to be taken into account in future vaccination strategies. Additionally, they highlight the importance of the genomic epidemiology of emerging pathogens in Africa and call for the implementation of a pan-African network for genomic surveillance of dengue virus.