In March 2014, the World Health Organization was notified of an outbreak of a communicable disease characterized by fever, severe diarrhea, vomiting, and a high fatality rate in Guinea. Virologic investigation identified Zaire ebolavirus (EBOV) as the causative agent. Full-length genome sequencing and phylogenetic analysis showed that EBOV from Guinea forms a separate clade in relationship to the known EBOV strains from the Democratic Republic of Congo and Gabon. Epidemiologic investigation linked the laboratory-confirmed cases with the presumed first fatality of the outbreak in December 2013. This study demonstrates the emergence of a new EBOV strain in Guinea.

Background An Ebola Virus Disease (EVD) epidemic of unprecedented magnitude is ongoing in West Africa, affecting for the first time large urban centers like Conakry, the capital of Guinea. Methods Interviews of EVD patients, relatives and neighbors and laboratory databases were used to reconstruct EVD chains of transmission in Conakry, from March to August 2014. Findings Out of 193 confirmed and probable EVD cases reported in Conakry, Boffa and Télimélé, 152 (79%) were positioned in the chains of transmission. In March, non-Health Care Workers cases infected on average 2.3 (95% CI: 1.6, 3.2) persons, breaking down into 1.4 (95% CI: 0.9, 2.2) persons in the community, 0.4 (95% CI: 0.1, 0.9) in the hospital and 0.5 (95% CI: 0.2, 1.0) at funerals. Following implementation of infection control in April, the reproduction number in the hospital and at funerals reduced below 0.1. In the community, the reproduction number, which was positively correlated with patients viremia, dropped by 50% for hospitalized cases but remained unchanged for those not hospitalized. Hospital and funeral transmission represented 35% (7/20) and 15% (3/20) of all transmissions in March; but only 9% (11/128) and 4% (5/128) from April onward. Overall, 82% (119/145) of transmission occurred in the community and 72% (105/145) between family members. Simulations showed that a 10% increase in hospitalizations could have reduced the length of chains by 26% (95% CI: 4%, 45%). Interpretation Monitoring chains of transmission is critical to evaluate and optimize local control strategies for EVD. In Conakry, interventions had the potential to stop the epidemic but reintroductions of the disease and lack of cooperation of a small number of families led to prolonged low-level spread, highlighting challenges of EVD control in large urban centers. Funding Labex IBEID, Reacting, PREDEMICS, NIGMS MIDAS initiative, Institut Pasteur de Dakar.

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.

Based on empiric surveillance data, the incidence of human Lassa fever (LF) cases in Guinea and other West African countries has been reported to increase during the dry season compared to the rainy season. To investigate possible links with the ecology of the rodent reservoir of the virus, we conducted a 2-year longitudinal survey of Mastomys natalensis in a region of high human Lassa virus (LASV) seropositivity in Guinea. Standardized rodent trapping with similar trapping efforts between seasons was performed in three villages and 53.5% (601/1123) of the animals were identified as M. natalensis using morphometric and molecular criteria. Mean trapping success (TS) of M. natalensis was always higher inside houses than in proximal cultivations. In the dry season, mean TS increased 2-fold inside houses and decreased up to 10-fold outside (p < 0.0001), suggesting aggregation of rodents inside houses due to restricted food supply. 14.5% (80/553) of M. natalensis were tested positive for Lassa virus by reverse transcription-polymerase chain reaction (RT-PCR; range, 5%-30%) and prevalence of the virus was two to three times higher in rodents captured in the rainy season than in the dry season (p < 0.05). Inside houses, however, the LASV prevalence fluctuated nonsignificantly with season. These data suggest that in Guinea the risk of LASV transmission from rodents to humans is present both in the rainy and the dry season, reflected by the occurrence of LF cases throughout the year. In the dry season, however, the increased risk of humans encountering Mastomys and their excreta inside of houses may result in an increase of human Lassa fever cases.

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.