Field investigation with real-time virus genetic characterisation support of a cluster of Ebola virus disease cases in Dubréka, Guinea, April to June 2015

How has Guinea learnt from the response to outbreaks? A learning health system analysis

INTRODUCTION

Learning is a key attribute of a resilient health system and, therefore, is central to health system strengthening. The main objective of this study was to analyse how Guinea's health system has learnt from the response to outbreaks between 2014 and 2021.

METHODS

We used a retrospective longitudinal single embedded case study design, applying the framework conceptualised by Sheikh and Abimbola for analysing learning health systems. Data were collected employing a mixed methods systematic review carried out in March 2022 and an online survey conducted in April 2022.

RESULTS

The 70 reports included in the evidence synthesis were about the 2014-2016 Ebola virus disease (EVD), Measles, Lassa Fever, COVID-19, 2021 EVD and Marburg virus disease. The main lessons were from 2014 to 2016 EVD and included: early community engagement in the response, social mobilisation, prioritising investment in health personnel, early involvement of anthropologists, developing health infrastructure and equipment and ensuring crisis communication. They were learnt through information (research and experts' opinions), action/practice and double-loop and were progressively incorporated in the response to future outbreaks through deliberation, single-loop, double-loop and triple-loop learning. However, advanced learning aspects (learning through action, double-loop and triple-loop) were limited within the health system. Nevertheless, the health system successfully controlled COVID-19, the 2021 EVD and Marburg virus disease. Survey respondents' commonly reported that enablers were the creation of the national agency for health security and support from development partners. Barriers included cultural and political issues and lack of funding. Common recommendations included establishing a knowledge management unit within the Ministry of Health with representatives at regional and district levels, investing in human capacities and improving the governance and management system.

CONCLUSION

Our study highlights the importance of learning. The health system performed well and achieved encouraging and better outbreak response outcomes over time with learning that occurred.

Optimized phylogenetic clustering of HIV-1 sequence data for public health applications

Clusters of genetically similar infections suggest rapid transmission and may indicate priorities for public health action or reveal underlying epidemiological processes. However, clusters often require user-defined thresholds and are sensitive to non-epidemiological factors, such as non-random sampling. Consequently the ideal threshold for public health applications varies substantially across settings. Here, we show a method which selects optimal thresholds for phylogenetic (subset tree) clustering based on population. We evaluated this method on HIV-1 pol datasets (n = 14, 221 sequences) from four sites in USA (Tennessee, Washington), Canada (Northern Alberta) and China (Beijing). Clusters were defined by tips descending from an ancestral node (with a minimum bootstrap support of 95%) through a series of branches, each with a length below a given threshold. Next, we used pplacer to graft new cases to the fixed tree by maximum likelihood. We evaluated the effect of varying branch-length thresholds on cluster growth as a count outcome by fitting two Poisson regression models: a null model that predicts growth from cluster size, and an alternative model that includes mean collection date as an additional covariate. The alternative model was favoured by AIC across most thresholds, with optimal (greatest difference in AIC) thresholds ranging 0.007-0.013 across sites. The range of optimal thresholds was more variable when re-sampling 80% of the data by location (IQR 0.008 - 0.016, n = 100 replicates). Our results use prospective phylogenetic cluster growth and suggest that there is more variation in effective thresholds for public health than those typically used in clustering studies.

Generating Uniformly Cross-Reactive Ebolavirus spp. Anti-nucleoprotein Nanobodies to Facilitate Forward Capable Detection Strategies

It is often challenging for a single monoclonal antibody to cross-react equally with all species of a particular viral genus that are separated by time and geographies to ensure broad long-term global immunodiagnostic use. Here, we set out to isolate nanobodies or single-domain antibodies (sdAbs) with uniform cross-reactivity to the genus Ebolavirus by immunizing a llama with recombinant nucleoprotein (NP) representing the 5 cultivated species to assemble a phage display repertoire for mining. Screening sdAbs for reactivity against the C-terminal domain of NP guided the isolation of clones that could perform as both captor and tracer for polyvalent antigen in sandwich assays. Two promising sdAbs had equivalent reactivities across all 5 species and greatly enhanced the equilibrium concentration at 50% (EC₅₀) for recombinant NP when compared with a differentially cross-reactive nonimmune sdAb isolated previously. Uniform reactivity and enhanced sensitivity were relayed to live virus titrations, resulting in lower limits of detection of 2-5 pfu for the best sdAbs, representing 10-, 20-, and 100-fold improvements for Zaire, Sudan/Reston, and Taï Forest viruses, respectively. Fusions of the sdAbs with ascorbate peroxidase (APEX2) and mNeonGreen generated one-step immunoreagents useful for colorimetric and fluorescent visualization of cellular NP. Both sdAbs were also able to recognize recombinant NPs from the recently discovered Bombali virus, a putative sixth Ebolavirus species unknown at the start of these experiments, validating the forward capabilities of the sdAbs. The simplicity and modularity of these sdAbs should enable advances in antigen-based diagnostic technologies to be retuned toward filoviral detection relatively easily, thereby proactively safeguarding human health.

Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks

Seven years after the declaration of the first epidemic of Ebola virus disease in Guinea, the country faced a new outbreak-between 14 February and 19 June 2021-near the epicentre of the previous epidemic^1,2. Here we use next-generation sequencing to generate complete or near-complete genomes of Zaire ebolavirus from samples obtained from 12 different patients. These genomes form a well-supported phylogenetic cluster with genomes from the previous outbreak, which indicates that the new outbreak was not the result of a new spillover event from an animal reservoir. The 2021 lineage shows considerably lower divergence than would be expected during sustained human-to-human transmission, which suggests a persistent infection with reduced replication or a period of latency. The resurgence of Zaire ebolavirus from humans five years after the end of the previous outbreak of Ebola virus disease reinforces the need for long-term medical and social care for patients who survive the disease, to reduce the risk of re-emergence and to prevent further stigmatization.

Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Sequencing the viral genome as the outbreak progresses is important, particularly in the identification of emerging isolates with different pathogenic potential and to identify whether nucleotide changes in the genome will impair clinical diagnostic tools such as real-time PCR assays. Although single nucleotide polymorphisms and point mutations occur during the replication of coronaviruses, one of the biggest drivers in genetic change is recombination. This can manifest itself in insertions and/or deletions in the viral genome. Therefore, sequencing strategies that underpin molecular epidemiology and inform virus biology in patients should take these factors into account. A long amplicon/read length-based RT-PCR sequencing approach focused on the Oxford Nanopore MinION/GridION platforms was developed to identify and sequence the SARS-CoV-2 genome in samples from patients with or suspected of COVID-19. The protocol, termed Rapid Sequencing Long Amplicons (RSLAs) used random primers to generate cDNA from RNA purified from a sample from a patient, followed by single or multiplex PCRs to generate longer amplicons of the viral genome. The base protocol was used to identify SARS-CoV-2 in a variety of clinical samples and proved sensitive in identifying viral RNA in samples from patients that had been declared negative using other nucleic acid-based assays (false negative). Sequencing the amplicons revealed that a number of patients had a proportion of viral genomes with deletions.

Clinical and epidemiological performance of WHO Ebola case definitions: a systematic review and meta-analysis

BACKGROUND

Ebola virus disease case definition is a crucial surveillance tool to detect suspected cases for referral and as a screening tool for clinicians to support admission and laboratory testing decisions at Ebola health facilities. We aimed to assess the performance of the WHO Ebola virus disease case definitions and other screening scores.

METHODS

In this systematic review and meta-analysis, we searched PubMed, Scopus, Embase, and Web of Science for studies published in English between June 13, 1978, and Jan 14, 2020. We included studies that estimated the sensitivity and specificity of WHO Ebola virus disease case definitions, clinical and epidemiological characteristics (symptoms at admission and contact history), and predictive risk scores against the reference standard (laboratory-confirmed Ebola virus disease). Summary estimates of sensitivity and specificity were calculated using bivariate and hierarchical summary receiver operating characteristic (when four or more studies provided data) or random-effects meta-analysis (fewer than four studies provided data).

FINDINGS

We identified 2493 publications, of which 14 studies from four countries (Sierra Leone, Guinea, Liberia, and Angola) were included in the analysis. 12 021 people with suspected disease were included, of whom 4874 were confirmed as positive for Ebola virus infection. Six studies explored the performance of WHO case definitions in non-paediatric populations, and in all of these studies, suspected and probable cases were combined and could not be disaggregated for analysis. The pooled sensitivity of the WHO Ebola virus disease case definitions from these studies was 81·5% (95% CI 74·1-87·2) and pooled specificity was 35·7% (28·5-43·6). History of contact or epidemiological link was a key predictor for the WHO case definitions (seven studies) and for risk scores (six studies). The most sensitive symptom was intense fatigue (79·0% [95% CI 74·4-83·0]), assessed in seven studies, and the least sensitive symptom was pain behind the eyes (1·0% [0·0-7·0]), assessed in three studies. The performance of fever as a symptom varied depending on the cutoff used to define fever.

INTERPRETATION

WHO Ebola virus disease case definitions perform suboptimally to identify cases at both community level and during triage at Ebola health facilities. Inclusion of intense fatigue as a key symptom and contact history could improve the performance of case definitions, but implementation of these changes will require effective collaboration with, and trust of, affected communities.

FUNDING

Médecins sans Frontières.

Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations

One of the key challenges in the field of genetics is the inference of haplotypes from next generation sequencing data. The MinION Oxford Nanopore sequencer allows sequencing long reads, with the potential of sequencing complete genes, and even complete genomes of viruses, in individual reads. However, MinION suffers from high error rates, rendering the detection of true variants difficult. Here, we propose a new statistical approach named AssociVar, which differentiates between true mutations and sequencing errors from direct RNA/DNA sequencing using MinION. Our strategy relies on the assumption that sequencing errors will be dispersed randomly along sequencing reads, and hence will not be associated with each other, whereas real mutations will display a non-random pattern of association with other mutations. We demonstrate our approach using direct RNA sequencing data from evolved populations of the MS2 bacteriophage, whose small genome makes it ideal for MinION sequencing. AssociVar inferred several mutations in the phage genome, which were corroborated using parallel Illumina sequencing. This allowed us to reconstruct full genome viral haplotypes constituting different strains that were present in the sample. Our approach is applicable to long read sequencing data from any organism for accurate detection of bona fide mutations and inter-strain polymorphisms.

Reporting quality of the 2014 Ebola outbreak in Africa: A systematic analysis

The objective of this study was to conduct a systematic analysis of the reporting quality of the Ebola Virus Disease (EVD) outbreak in West Africa from 2014-2018 using the Modified STROBE statement. We included studies on the 2014 EVD outbreak alone, limited to those on human patients in Africa. We searched the following databases (MEDLINE, EMBASE, and Web of Science) for outbreak reports published between 2014-2018. We assessed factors potentially associated with the quality of reporting. A total of 69 of 131 (53%) articles within the full-text review fulfilled our eligibility criteria and underwent the Modified STROBE assessment for analyzing the quality of reporting. The Modified STROBE scores of the included studies ranged from 11-26 points and the mean was found to be 19.54 out of 30 with a standard deviation (SD) of ± 4.30. The top three reported Modified STROBE components were descriptive characteristics of study participants, scientific background and evidence rational, and clinical significance of observations. More than 75% of the studies met a majority of the criteria in the Modified STROBE assessment tool. Information that was commonly missing included addressing potential source of bias, sensitivity analysis, further results/analysis such as risk estimates and odds ratios, presence of a flowchart, and addressing missing data. In multivariable analysis, peer-reviewed publication was the only predictor that remained significantly associated with a higher Modified STROBE score. In conclusion, the large range of Modified STROBE scores observed indicates variability in the quality of outbreak reports for EVD. The review identified strong reporting in some areas, whereas other areas are in need of improvement, in particular providing an important description of the outbreak setting and identifying any external elements (potential biases and confounding factors) that could hinder the credibility of the findings.

Challenges and perspectives on the use of mobile laboratories during outbreaks and their use for vaccine evaluation

Mobile laboratories provide diagnostic capabilities for routine surveillance and patient identification during an outbreak. In either situation, they face many challenges including identification of the appropriate assay(s) to employ, logistical arrangements, and providing for the health and safety of the laboratory staff. Great strides have been made over the last decade in the development of mobile laboratories with assays that require minimal infrastructure and technical experience. This knowledge and expertise have been developed in partnership with many researchers and public health officials who live in regions prone to infectious disease outbreaks. Mobile laboratories should now also be used in the evaluation of novel vaccines and therapeutics in remote locations. Clinical mobile laboratories will include similar diagnostic capabilities as outbreak response mobile labs, but will also include additional point-of-care instruments operated under Good Clinical Practice guidelines. They will also operate rigorous data management plans so that the data collected will satisfy regulatory agencies during the licensure process. Failure to deploy an adequate clinical mobile laboratory when administering a novel biological product in a remote location is a significant limitation to any collected scientific data that could ultimately undermine clinical development and availability of life-saving interventions.