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Summary Background Between 2014 and 2017, successive cholera epidemics occurred in South Sudan within the context of civil war, population displacement, flooding, and drought. We aim to describe the spatiotemporal and molecular features of the three distinct epidemic waves and explore the role of vaccination campaigns, precipitation, and population movement in shaping cholera spread in this complex setting. Methods In this descriptive epidemiological study, we analysed cholera linelist data to describe the spatiotemporal progression of the epidemics. We placed whole-genome sequence data from pandemic Vibrio cholerae collected throughout these epidemics into the global phylogenetic context. Using whole-genome sequence data in combination with other molecular attributes, we characterise the relatedness of strains circulating in each wave and the region. We investigated the association of rainfall and the instantaneous basic reproduction number using distributed lag non-linear models, compared county-level attack rates between those with early and late reactive vaccination campaigns, and explored the consistency of the spatial patterns of displacement and suspected cholera case reports. Findings The 2014 (6389 cases) and 2015 (1818 cases) cholera epidemics in South Sudan remained spatially limited whereas the 2016–17 epidemic (20 438 cases) spread among settlements along the Nile river. Initial cases of each epidemic were reported in or around Juba soon after the start of the rainy season, but we found no evidence that rainfall modulated transmission during each epidemic. All isolates analysed had similar genotypic and phenotypic characteristics, closely related to sequences from Uganda and Democratic Republic of the Congo. Large-scale population movements between counties of South Sudan with cholera outbreaks were consistent with the spatial distribution of cases. 21 of 26 vaccination campaigns occurred during or after the county-level epidemic peak. Counties vaccinated on or after the peak incidence week had 2·2 times (95% CI 2·1–2·3) higher attack rates than those where vaccination occurred before the peak. Interpretation Pandemic V cholerae of the same clonal origin was isolated throughout the study period despite interepidemic periods of no reported cases. Although the complex emergency in South Sudan probably shaped some of the observed spatial and temporal patterns of cases, the full scope of transmission determinants remains unclear. Timely and well targeted use of vaccines can reduce the burden of cholera; however, rapid vaccine deployment in complex emergencies remains challenging. Funding The Bill & Melinda Gates Foundation.

MenAfriVac™ is a conjugate vaccine against meningitis A specifically designed for Africa. In Niger, the MenAfriVac™ vaccination campaign was conducted in people aged 1-29 years in three phases. The third phase was conducted in November/December 2011 targeting more than 7 million people. We estimated vaccination coverage for the third phase; classified the 31 target districts according to vaccination coverage levels; analysed the factors associated with being vaccinated; described the reasons for non-vaccination; and estimated coverage of the MenAfriVac™ introduction in Niger by aggregating data from all three phases. We classified the districts by clustered lot quality assurance sampling according to a 75% lower threshold and a 90% upper threshold. We estimated coverage using a minimum cluster-sample of 30 x 10 in each region. Two criteria were used to document vaccination status: presentation of vaccination card only or by card and/or verbal history of vaccination (card+history). We surveyed 2390 persons. After the third phase, estimated coverage was 68.8% (95% CI 64.9-72.8) by card only and 90.9% (95% CI 88.6-93.2) by card+history. Five districts were accepted for coverage above 75% based on card only, whereas 25 were accepted based on card+history. Factors positively associated with being vaccinated were younger age (15 years), female sex, residing in the same household for more than three months, and being informed about the vaccination campaign. The main reason for non-vaccination was not being at home during the campaign. Overall coverage for MenAfriVac™ introduction via 3 phases was 76.1% (95% CI: 72.5-79.6) by card only and 91.9% (95%CI: 89.7-94.1) by card+history.Although estimated coverage was high, pockets of non-vaccination probably still exist in the country; thus, the implementation of mop-up campaigns should be considered. Priorities for the future should include incorporating meningitis A vaccination into the existing immunization schedule and assessing its impact at a population level.

MenAfriVac™ is a new meningococcal A conjugate vaccine developed to prevent meningitis outbreaks in Africa. It was first introduced during the last quarter of 2010 in three West African countries. We report on the monitoring of adverse events following immunization (AEFI) in Burkina Faso where more than 11 million people aged 1-29 years were vaccinated. Vaccine pharmacovigilance relied on stimulated passive AEFI surveillance countrywide and active surveillance for 12 clinical conditions in one sentinel district (Ziniaré) with 97,715 people eligible for vaccination. All AEFI occurring during the 10 days of mass campaign or the 42 subsequent days were to be notified. Serious AEFI were submitted to a national expert committee (NEC) for causality assessment. A total of 11,466,950 people were vaccinated with 1471 vaccinees reported to have experienced at least one AEFI (12.83 cases per 100,000). 1444 AEFI were minor; the most common of which were fever, headache, gastro-intestinal disorders and local reactions (2-7 cases per 100,000). Of 27 serious AEFI reported, four cases were classified by the NEC as related to vaccine (1 case per 3 million vaccinated) including one case each of exanthematous pustulosis, angioedema, bronchospasm and severe vomiting. Active surveillance identified 71 cases of the 12 conditions of interest. Convulsions, urticaria and bronchospasm were more frequently reported. Attack rates for those conditions were similar to the baseline rates recorded in the same population, over the same time period, a year earlier. With the exception of convulsions in the days following vaccination the distribution of time intervals between vaccination and the occurrence of symptoms did not reveal any temporal clustering. The monitoring of AEFI of MenAfriVac™ in Burkina Faso did not suggest special concern regarding the vaccine safety. However, reported possible hypersensitivity reactions to vaccine components would require further review to rule out any anaphylactic reaction.