Deployment of the Institut Pasteur de Dakar team to Guinea in the Ebola virus Disease outbreak in West-Africa 2014-2016

First paragraph: The unit of Arbovirus and Haemorrhagic Fever Viruses at the Institut Pasteur de Dakar (IPD), a WHO-approved collaborating Centre was the first laboratory deployed to Conakry in the Ebola virus disease (EVD) outbreak in West-Africa. On 20 March 2014, the IPD laboratory received a letter from the WHO and the Guinean Ministry of Health, informing about a suspected haemorrhagic fever outbreak and difficulties to send collected samples to IPD. They therefore requested the deployment of experts to Guinea for technical support in order to diagnose the haemorrhagic fever of unknown origin. The outbreak was identified by the Institut Pasteur (France) on 21 March 2014 [1,2] in samples shipped to France by a Médecins sans Frontières investigation team

Morphological, genetical and ecological discrimination of sympatric Coastal Guinea Mastomys (Mammalia : Rodentia) species (West Africa) : implications for health and agriculture

Cytogenetic and molecular tools have shown the existence of two sibling species of the multimammate rat in Coastal Guinea : M. erythroleucus and M. huberti from Mankoutan locality. Here we present the study of the unique population of M. huberti ever recorded in Guinea, distant from 350 km from the closest locality in Senegal and representing the southernmost point of the species’ disjunct distribution. In order to clarify its ecological preferences and define its degree of sympatry with M. erythroleucus, we have searched for morphological and morphometric criteria allowing reliable identification of the species in Coastal Guinea. Discriminant Factorial Analyses (DFA) were performed on external and skull measurements for respectively 108 and 106 previously genetically typed individuals. All discriminant analyses showed that the 100 % rate of good classification is never attained. Misclassifications of 55.6 % of the specimens were obtained in the field by using external fur colour and aspect whereas the error score ranged from 4.5 to 8 % by using DFA on external measurements. Furthermore, DFA on skull measurements gave 100 % of correct classification for M. huberti - which is characterized by a smaller size - against 96.97 % for M. erythroleucus. In the same time, we were able to define the local specific habitat of each species. In Mankountan, M. huberti is never found into houses but prefers wet rice fields, while M. erythroleucus is found both in houses and cultures as well as in wet rice fields where it is found in syntopy with M. huberti at the end of the dry season. In Yerende, a hundred kilometres from Mankoutan, we only caught M. erythroleucus both in houses and fields. This study once again highlights the importance of a deep taxonomic knowledge of small mammals’ diversity for sanitary and agricultural risks evaluation but also confirms the problems of identification encountered with rodent sibling species living in sympatryLes analyses cytogénétiques et moléculaires ont mis en évidence la présence de deux espèces jumelles de Mastomys en Guinée Maritime: M. ervthroleucus et M. huberti dans la localité de Mankoutan. Il s'agit de la première étude de la seule population de M. huberti rencontrée en Guinée située à 350 km de la population la plus proche du Sénégal, à l'extrémité Sud de l'aire de distribution disjointe de l'espèce. Afin de définir ses préférences écologiques, nous avons recherché des critères morphologiques et morphométriques pour identifier les deux espèces de Mastomys afin de mieux définir leur degré de sympa-trie. Des Analyses Factorielles Discriminantes (AFD) effectuées sur les caractères externes et crâniens de 108 et 106 individus ayant fait l'objet d'analyses moléculaires (cyt.b) et /ou cytogénétiques, provenant de deux localités proches, montrent que l'on ne peut jamais discriminer avec 100 % de certitude les spécimens en 'peau' et 'crâne'. Le taux d'erreur de détermination des deux espèces atteint 55,6 % pour la coloration et l'aspect du pelage sur le terrain, il oscille entre 4,5 et 8 % en AFD sur les mesures externes. Cependant avec les mesures crâniennes traitées par AFD, les M. huberti se distinguent à 100 % par une taille légèrement plus faible, contre 96,97 % chez M. erythroleucus. Parallèlement, nous avons pu préciser l'habitat spécifique aux deux espèces dans la même localité. Ainsi, à Mankountan, M. huberti n'est jamais rencontré dans les maisons et préfère les champs de riz inondés. M. erythroleucus est présent à la fois dans les maisons et dans les champs, quelquefois dans les rizières inondés où, à la fin de la saison sèche, il se retrouve en syntopie avec M. huberti. La localité de Yerendé située à 100 km de Mankountan n'a livré que des M. erythroleucus, présents à la fois dans les maisons et les champs. Cette étude montre l'importance d'une connaissance approfondie de la systématique et de la diversité des petits mammifères nuisibles pour l'évaluation des risques sanitaires et agricoles et confirme les difficultés d'identification morphologique des espèces jumelles chez les rongeurs

Experiences of outbreak laboratory management in the Ebola Disease outbreak in West-Africa 2014-2015

During the Ebola Disease outbreak in 2014-2015 West-Africa about 24 organizations operated laboratories at 40 sites in Guinea, Sierra Leone and Liberia. Representatives of ten organisations which had deployed laboratories to 16 sites across the three countries in West-Africa convened for a two day symposium in Dakar (4-5.02.16) to exchange their experiences. This article summarizes the discussion and points made during the discussion of the laboratory deployment experiences during the epidemic touching organisational and procedural issues.Additional co-authors: P Jansen van Vuren, K Stroecker, J Paweska, C Picard, H Sheeley, P Smit, AA Sal

Molecular Diagnostics of Ebola Patient Samples by Institut Pasteur de Dakar Mobile Laboratory in Guinea 2014–2016

As part of the laboratory response to the Ebola virus outbreak in Guinea, the Institut Pasteur de Dakar mobile laboratory (IPD-ML) was set up in Donka hospital from 2014 to 2016. EBOV suspected samples collected at Ebola Treatment Centers (ETC) and from community deaths were sent daily to IPD-ML. Analysis was performed using dried oligonucleotide mixes for real-time RT-PCR designed for field diagnostic. From March 2014 to May 2015, a total of 6055 patient samples suspected for EBOV collected from seven regions of Guinea were tested by real-time RT-PCR. These patients’ clinical included serum samples (n = 2537 samples) and swabs (n = 3518 samples) with positivity rates of 36.74 and 6.88% respectively. Females were significantly more affected than males with positivity rates of 22.39 and 17.22% respectively (p-value = 5.721e-7). All age groups were exposed to the virus with significant difference (p-value <= 2.2e-16). The IPD-ML contributed significantly to the surveillance and patient management during the EBOV outbreak in Guinea. Furthermore, dried reagents adapted for field diagnostic of EVD suspect cases could be useful for future outbreak preparedness and response

Development and deployment of a rapid recombinase polymerase amplification Ebola virus detection assay in Guinea in 2015

In the absence of a vaccine or specific treatments for Ebola virus disease (EVD), early identification of cases is crucial for the control of EVD epidemics. We evaluated a new extraction kit (SpeedXtract (SE), Qiagen) on sera and swabs in combination with an improved diagnostic reverse transcription recombinase polymerase amplification assay for the detection of Ebola virus (EBOV-RT-RPA). The performance of combined extraction and detection was best for swabs. Sensitivity and specificity of the combined SE and EBOV-RT-RPA were tested in a mobile laboratory consisting of a mobile glovebox and a Diagnostics-in-a-Suitcase powered by a battery and solar panel, deployed to Matoto Conakry, Guinea as part of the reinforced surveillance strategy in April 2015 to reach the goal of zero cases. The EBOV-RT-RPA was evaluated in comparison to two real-time PCR assays. Of 928 post-mortem swabs, 120 tested positive, and the combined SE and EBOV-RT-RPA yielded a sensitivity and specificity of 100% in reference to one real-time RT-PCR assay. Another widely used real-time RT-PCR was much less sensitive than expected. Results were provided very fast within 30 to 60 min, and the field deployment of the mobile laboratory helped improve burial management and community engagement.Additional co-authors: Ali Mirazimi, Oliver Nentwich, Olaf Piepenburg, Matthias Niedrig, Amadou Alpha Sal

Hantavirus in African Wood Mouse, Guinea

Hantaviruses are rodentborne, emerging viruses that cause life-threatening human diseases in Eurasia and the Americas. We detected hantavirus genome sequences in an African wood mouse (Hylomyscus simus) captured in Sangassou, Guinea. Sequence and phylogenetic analyses of the genetic material demonstrate a novel hantavirus species, which we propose to name "Sangassou virus.

Mastomys natalensis and Lassa Fever, West Africa

PCR screening of 1,482 murid rodents from 13 genera caught in 18 different localities of Guinea, West Africa, showed Lassa virus infection only in molecularly typed Mastomys natalensis. Distribution of this rodent and relative abundance compared with M. erythroleucus correlates geographically with Lassa virus seroprevalence in humans

Use of Viremia to Evaluate the Baseline Case Fatality Ratio of Ebola Virus Disease and Inform Treatment Studies: A Retrospective Cohort Study.

BACKGROUND: The case fatality ratio (CFR) of Ebola virus disease (EVD) can vary over time and space for reasons that are not fully understood. This makes it difficult to define the baseline CFRs needed to evaluate treatments in the absence of randomized controls. Here, we investigate whether viremia in EVD patients may be used to evaluate baseline EVD CFRs. METHODS AND FINDINGS: We analyzed the laboratory and epidemiological records of patients with EVD confirmed by reverse transcription PCR hospitalized in the Conakry area, Guinea, between 1 March 2014 and 28 February 2015. We used viremia and other variables to model the CFR. Data for 699 EVD patients were analyzed. In the week following symptom onset, mean viremia remained stable, and the CFR increased with viremia, V, from 21% (95% CI 16%-27%) for low viremia (V < 104.4 copies/ml) to 53% (95% CI 44%-61%) for intermediate viremia (104.4 ≤ V < 105.2 copies/ml) and 81% (95% CI 75%-87%) for high viremia (V ≥ 105.2 copies/ml). Compared to adults (15-44 y old [y.o.]), the CFR was larger in young children (0-4 y.o.) (odds ratio [OR]: 2.44; 95% CI 1.02-5.86) and older adults (≥ 45 y.o.) (OR: 2.84; 95% CI 1.81-4.46) but lower in children (5-14 y.o.) (OR: 0.46; 95% CI 0.24-0.86). An order of magnitude increase in mean viremia in cases after July 2014 compared to those before coincided with a 14% increase in the CFR. Our findings come from a large hospital-based study in Conakry and may not be generalizable to settings with different case profiles, such as with individuals who never sought care. CONCLUSIONS: Viremia in EVD patients was a strong predictor of death that partly explained variations in CFR in the study population. This study provides baseline CFRs by viremia group, which allow appropriate adjustment when estimating efficacy in treatment studies. In randomized controlled trials, stratifying analysis on viremia groups could reduce sample size requirements by 25%. We hypothesize that monitoring the viremia of hospitalized patients may inform the ability of surveillance systems to detect EVD patients from the different severity strata

Creating a National Specimen Referral System in Guinea: Lessons From Initial Development and Implementation

In the wake of the 2014–2016, West Africa Ebola virus disease (EVD) outbreak, the Government of Guinea recognized an opportunity to strengthen its national laboratory system, incorporating capacity and investments developed during the response. The Ministry of Health (MOH) identified creation of a holistic, safe, secure, and timely national specimen referral system as a priority for improved detection and confirmation of priority diseases, in line with national Integrated Disease Surveillance and Response guidelines. The project consisted of two parts, each led by different implementing partners working collaboratively together and with the Ministry of Health: the development and approval of a national specimen referral policy, and pilot implementation of a specimen referral system, modeled on the policy, in three prefectures. This paper describes the successful execution of the project, highlighting the opportunities and challenges of building sustainable health systems capacity during and after public health emergencies, and provides lessons learned for strengthening national capabilities for surveillance and disease diagnosis