Medical trainees face multiple barriers to participation in major outbreak responses such as that required for Ebola Virus Disease through 2014-2015 in West Africa. Hurdles include fear of contracting and importing the disease, residency requirements, scheduling conflicts, family obligations and lack of experience and maturity. We describe the successful four-week deployment to Liberia of a first year infectious diseases trainee through the mechanism of the Global Outbreak Alert and Response Network of the World Health Organization. The posting received prospective approval from the residency supervisory committees and employing hospital management and was designed with components fulfilling the Accreditation Council for Graduate Medical Education (ACGME) core competencies. It mirrored conventional training with regards to learning objectives, supervisory framework and assessment methods. Together with Centers for Disease Control and Prevention and many other partners, the team joined the infection prevention and control efforts in Monrovia. Contributions were made to a ‘ring fencing’ infection control approach that was being introduced, including enhancement of triage, training and providing supplies in high priority health-care facilities in the capital and border zones. In addition the fellow produced an electronic database that enabled monitoring infection control standards in health facilities. This successful elective posting illustrates that quality training can be achieved, even in the most challenging environments, with support from the pedagogic and sponsoring institutions. Such experiential learning opportunities benefit both the outbreak response and the trainee, and if scaled up would contribute towards building a global health emergency workforce. More should be done from residency accreditation bodies in facilitating postings in outbreak settings.
Chikungunya is an emerging arbovirus that is characterized into four lineages. One of these, the Asian genotype, has spread rapidly in the Americas after its introduction in the Saint Martin island in October 2013. Unexpectedly, a new lineage, the East-Central-South African genotype, was introduced from Angola in the end of May 2014 in Feira de Santana (FSA), the second largest city in Bahia state, Brazil, where over 5,500 cases have now been reported. Number weekly cases of clinically confirmed CHIKV in FSA were analysed alongside with urban district of residence of CHIKV cases reported between June 2014 and October collected from the municipality’s surveillance network. The number of cases per week from June 2014 until September 2015 reveals two distinct transmission waves. The first wave ignited in June and transmission ceased by December 2014. However, a second transmission wave started in January and peaked in May 2015, 8 months after the first wave peak, and this time in phase with Dengue virus and Zika virus transmission, which ceased when minimum temperature dropped to approximately 15°C. We find that shorter travelling times from the district where the outbreak first emerged to other urban districts of FSA were strongly associated with incidence in each district in 2014 (R2).
In the three West African countries most affected by the recent Ebola virus disease (EVD) outbreak, resistance to public health measures contributed to the startling speed and persistence of this epidemic in the region. But how do we explain this resistance, and how have people in these communities understood their actions? By comparing these recent events to historical precedents during Cholera outbreaks in Europe in the 19th century we show that these events have not been new to history or unique to Africa. Community resistance must be analysed in context and go beyond simple single-variable determinants. Knowledge and respect of the cultures and beliefs of the afflicted is essential for dealing with threatening disease outbreaks and their potential social violence.
Introduction and Methods: Pertussis has recently re-emerged in the United States. Timely surveillance is vital to estimate the burden of this disease accurately and to guide public health response. However, the surveillance of pertussis is limited by delays in reporting, consolidation and dissemination of data to relevant stakeholders. We fit and assessed a real-time predictive Google model for pertussis in California using weekly incidence data from 2009-2014.
Results and Discussion: The linear model was moderately accurate (r = 0.88). Our findings cautiously offer a complementary, real-time signal to enhance pertussis surveillance in California and help to further define the limitations and potential of Google-based epidemic prediction in the rapidly evolving field of digital disease detection.
Introduction: The ability to predict the growth and decline of infectious disease incidence has advanced considerably in recent years. In particular, accurate forecasts of influenza epidemiology have been developed using a number of approaches.
Methods: Within our own group we produce weekly operational real-time forecasts of influenza at the municipal and state level in the U.S. These forecasts are generated using ensemble simulations depicting local influenza transmission dynamics, which have been optimized prior to forecast with observations of influenza incidence and data assimilation methods. The expected accuracy of a given forecast can be inferred in real-time through quantification of the agreement (e.g. the variance) among the ensemble of simulations.
Results: Here we show that forecast expected accuracy can be further discriminated with the additional consideration of the streak or persistence of the forecast—the number of consecutive weeks the forecast has converged to the same outcome.
Discussion: The findings indicate that the use of both the streak and ensemble agreement provides a more detailed and informative assessment of forecast expected accuracy.
Introduction: In April and May 2014, two suspected egg-related outbreaks of Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) were investigated by the Belgian National Reference Laboratory of Foodborne Outbreaks. Both the suspected food and human isolates being available, and this for both outbreaks, made these the ideal case study for a retrospective whole genome sequencing (WGS) analysis with the goal to investigate the feasibility of this technology for outbreak investigation by a National Reference Laboratory or National Reference Centre without thorough bioinformatics expertise.
Methods: The two outbreaks were originally investigated epidemiologically with a standard questionnaire and with serotyping, phage typing, multiple-locus variable-number of tandem repeats analysis (MLVA) and antimicrobial susceptibility testing as classical microbiological methods. Retrospectively, WGS of six outbreak isolates was done on an Illumina HiSeq. Analysis of the WGS data was performed with currently available, user-friendly software and tools, namely CLC Genomics Workbench, the tools available on the server of the Center for Genomic Epidemiology and BLAST Ring Image Generator (BRIG).
Results: To all collected human and food outbreak isolates, classical microbiological investigation assigned phage type PT4 (variant phage type PT4a for one human isolate) and MLVA profile 3-10-5-4-1, both of which are common for human isolates in Belgium. The WGS analysis confirmed the link between food and human isolates for each of the outbreaks and clearly discriminated between the two outbreaks occurring in a same time period, thereby suggesting a non-common source of contamination. Also, an additional plasmid carrying an antibiotic resistance gene was discovered in the human isolate with the variant phage type PT4a.
Discussion: For the two investigated outbreaks occurring at geographically separated locations, the gold standard classical microbiological subtyping methods were not sufficiently discriminative to distinguish between or assign a common origin of contamination for the two outbreaks, while WGS analysis could do so. This case study demonstrated the added value of WGS for outbreak investigations by confirming and/or discriminating food and human isolates between and within outbreaks. It also proved the feasibility of WGS as complementary or even future replacing (sub)typing method for the average routine laboratory.
Introduction: The eradication of a human infectious disease is a major challenge and, if achieved, represents a enormous achievement. This article explores the long and difficult journey towards eradication for polio and guinea worm.
Methods: The authors reviewed the programmatic approaches taken in the eradication strategies for these two diseases and the unique socio-political contexts in which these strategies are couched. The epidemiology of the last 15 years is compared and contrasted. The specific challenges for both programs are outlined and some key elements for success are highlighted.
Discussion: The success of these eradication programs is contingent upon many factors. Nothing is assured, and progress remains fragile and vulnerable to setbacks. Security must be ensured in guinea worm transmission areas in Africa and polio transmission areas in Pakistan and Afghanistan. Technical solutions alone cannot guarantee eradication. National leadership and continued international focus and support are necessary, today more than ever. The legacy of success would be extraordinary. It would reverberate to future generations in the same way that the eradication of smallpox does for this generation.
Introduction: Further understanding of the genetic diversity and evolution of influenza A viruses circulating in swine (IAV-S) is important for the development of effective vaccines and our knowledge of pandemic threats. Until recently, very little was known of IAV-S diversity in Latin America, owing to a lack of surveillance.
Methods: To address this gap, we sequenced and conducted a phylogenetic analysis of 69 hemagglutinin (HA) sequences from IAV-S isolates collected in swine in Mexico and Chile during 2010-2014, including the H1N1, H1N2, and H3N2 subtypes.
Results: Our analysis identified multiple IAV-S lineages that appear to have been circulating undetected in swine for decades, including four novel IAV-S lineages of human seasonal virus origin that have not been previously identified in any swine populations globally. We also found evidence of repeated introductions of pandemic H1N1 viruses from humans into swine in Mexico and Chile since 2009, and incursions of H1 and H3 viruses from North American swine into Mexico.
Discussion: Overall, our findings indicate that at least 12 genetically distinct HA lineages circulate in Latin American swine herds, only two of which have been found in North American swine herds. Human-to-swine transmission, spatial migration via swine movements, and genomic reassortment are the key evolutionary mechanisms that generate this viral diversity. Additional antigenic characterization and whole-genome sequencing is greatly needed to understand the diversity and independent evolution of IAV-S in Latin America.
Participatory systems for surveillance of acute respiratory infection give real-time information about infections circulating in the community, yet to-date are limited to self-reported syndromic information only and lacking methods of linking symptom reports to infection types. We developed the GoViral platform to evaluate whether a cohort of lay volunteers could, and would find it useful to, contribute self-reported symptoms online and to compare specimen types for self-collected diagnostic information of sufficient quality for respiratory infection surveillance. Volunteers were recruited, given a kit (collection materials and customized instructions), instructed to report their symptoms weekly, and when sick with cold or flu-like symptoms, requested to collect specimens (saliva and nasal swab). We compared specimen types for respiratory virus detection sensitivity (via polymerase-chain-reaction) and ease of collection. Participants were surveyed to determine receptivity to participating when sick, to receiving information on the type of pathogen causing their infection and types circulating near them. Between December 1 2013 and March 1 2014, 295 participants enrolled in the study and received a kit. Of those who reported symptoms, half (71) collected and sent specimens for analysis. Participants submitted kits on average 2.30 days (95 CI: 1.65 to 2.96) after symptoms began. We found good concordance between nasal and saliva specimens for multiple pathogens, with few discrepancies. Individuals report that saliva collection is easiest and report that receiving information about what pathogen they, and those near them, have is valued and can shape public health behaviors. Community-submitted specimens can be used for the detection of acute respiratory infection with individuals showing receptivity for participating and interest in a real-time picture of respiratory pathogens near them.