Browsing by Author "Pulliam, Juliet R. C."
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- ItemComplete genome sequence of dengue virus serotype 2, Asian/American genotype, isolated from the urine of a Venezuelan child with hemorrhagic fever in 2016(American Society for Microbiology, 2018) Blohm, Gabriela M.; Paniz-Mondolfi, Alberto E.; Marquez, Marilianna C.; Loeb, Julia C.; Pacheco, Carlos; Lednicky, John A.; Pulliam, Juliet R. C.; Morris, J. GlennThe complete genome sequence was obtained for a Dengue virus 2 isolate from the urine of an 8-year-old girl who was hospitalized with dengue hemorrhagic fever in 2016 in Venezuela.
- ItemComplete genome sequences of identical zika virus isolates in a nursing mother and her infant(American Society for Microbiology, 2017) Blohm, Gabriela M.; Lednicky, John A.; Marquez, Marilianna; White, Sarah K.; Loeb, Julia C.; Pacheco, Carlos A.; Nolan, David J.; Paisie, Taylor; Salemi, Marco; Rodriguez-Morales, Alfonso J.; Morris, J. Glenn; Pulliam, Juliet R. C.; Carrillo, Alejandra S.; Plaza, Juan D.; Paniz-Mondolfi, Alberto E.ENGLISH ABSTRACT: Complete genome sequences were obtained for Zika viruses isolated from the breast milk of a Venezuelan patient and her child, who was exclusively breastfeeding at the time. These sequences are the first to be reported from a presumptive autochthonous postnatal transmission case from mother to child in Venezuela.
- ItemEmerging infectious diseases and biological invasions : a call for a One Health collaboration in science and management(Royal Society, 2019) Ogden, Nick H.; Wilson, John R. U.; Richardson, David M.; Hui, Cang; Davies, Sarah J.; Kumschick, Sabrina; Le Roux, Johannes J.; Measey, John; Saul, Wolf-Christian; Pulliam, Juliet R. C.The study and management of emerging infectious diseases (EIDs) and of biological invasions both address the ecology of human-associated biological phenomena in a rapidly changing world. However, the two fields work mostly in parallel rather than in concert. This review explores how the general phenomenon of an organism rapidly increasing in range or abundance is caused, highlights the similarities and differences between research on EIDs and invasions, and discusses shared management insights and approaches. EIDs can arise by: (i) crossing geographical barriers due to human-mediated dispersal, (ii) crossing compatibility barriers due to evolution, and (iii) lifting of environmental barriers due to environmental change. All these processes can be implicated in biological invasions, but only the first defines them. Research on EIDs is embedded within the One Health concept—the notion that human, animal and ecosystem health are interrelated and that holistic approaches encompassing all three components are needed to respond to threats to human well-being. We argue that for sustainable development, biological invasions should be explicitly considered within One Health. Management goals for the fields are the same, and direct collaborations between invasion scientists, disease ecologists and epidemiologists on modelling, risk assessment, monitoring and management would be mutually beneficial.
- ItemEpidemic curves made easy using the R package incidence [version 1; peer review : 1 approved, 2 approved with reservations](F1000Research, 2019) Kamvar, Zhian N.; Cai, Jun; Pulliam, Juliet R. C.; Schumacher, Jakob; Jombart, ThibautThe epidemiological curve (epicurve) is one of the simplest yet most useful tools used by field epidemiologists, modellers, and decision makers for assessing the dynamics of infectious disease epidemics. Here, we present the free, open-source package incidence for the R programming language, which allows users to easily compute, handle, and visualise epicurves from unaggregated linelist data. This package was built in accordance with the development guidelines of the R Epidemics Consortium (RECON), which aim to ensure robustness and reliability through extensive automated testing, documentation, and good coding practices. As such, it fills an important gap in the toolbox for outbreak analytics using the R software, and provides a solid building block for further developments in infectious disease modelling.
- ItemHow to make epidemiological training infectious(Public Library of Science, 2012-04-03) Bellan, Steve E.; Pulliam, Juliet R. C.; Scott, James C.; Dushoff, Jonathan; Porco, T.; Williams, B. G.; Hargrove, J. W.Modern infectious disease epidemiology builds on two independently developed fields: classical epidemiology and dynamical epidemiology. Over the past decade, integration of the two fields has increased in research practice, but training options within the fields remain distinct with few opportunities for integration in the classroom. The annual Clinic on the Meaningful Modeling of Epidemiological Data (MMED) at the African Institute for Mathematical Sciences has begun to address this gap. MMED offers participants exposure to a broad range of concepts and techniques from both epidemiological traditions. During MMED 2010 we developed a pedagogical approach that bridges the traditional distinction between classical and dynamical epidemiology and can be used at multiple educational levels, from high school to graduate level courses. The approach is hands-on, consisting of a real-time simulation of a stochastic outbreak in course participants, including realistic data reporting, followed by a variety of mathematical and statistical analyses, stemming from both epidemiological traditions. During the exercise, dynamical epidemiologists developed empirical skills such as study design and learned concepts of bias while classical epidemiologists were trained in systems thinking and began to understand epidemics as dynamic nonlinear processes. We believe this type of integrated educational tool will prove extremely valuable in the training of future infectious disease epidemiologists. We also believe that such interdisciplinary training will be critical for local capacity building in analytical epidemiology as Africa continues to produce new cohorts of well-trained mathematicians, statisticians, and scientists. And because the lessons draw on skills and concepts from many fields in biology—from pathogen biology, evolutionary dynamics of host–pathogen interactions, and the ecology of infectious disease to bioinformatics, computational biology, and statistics—this exercise can be incorporated into a broad array of life sciences courses.
- ItemOutbreak response intervention models of vaccine-preventable diseases in humans and foot-and- mouth disease in livestock : a protocol for a systematic review(BMJ Publishing Group, 2020) Azam, James M.; Are, Elisha B.; Pang, Xiaoxi; Ferrari, Matthew J.; Pulliam, Juliet R. C.Introduction Outbreaks of vaccine-preventable diseases continue to threaten public health, despite the proven effectiveness of vaccines. Interventions such as vaccination, social distancing and palliative care are usually implemented, either individually or in combination, to control these outbreaks. Mathematical models are often used to assess the impact of these interventions and for supporting outbreak response decision making. The objectives of this systematic review, which covers all human vaccine-preventable diseases, are to determine the relative impact of vaccination compared with other outbreak interventions, and to ascertain the temporal trends in the use of modelling in outbreak response decision making. We will also identify gaps and opportunities for future research through a comparison with the foot-and- mouth disease outbreak response modelling literature, which has good examples of the use of modelling to inform outbreak response intervention decision making. Methods and analysis We searched on PubMed, Scopus, Web of Science, Google Scholar and some preprint servers from the start of indexing to 15 January 2020. Inclusion: modelling studies, published in English, that use a mechanistic approach to evaluate the impact of an outbreak intervention. Exclusion: reviews, and studies that do not describe or use mechanistic models or do not describe an outbreak. We will extract data from the included studies such as their objectives, model types and composition, and conclusions on the impact of the intervention. We will ascertain the impact of models on outbreak response decision making through visualisation of time trends in the use of the models. We will also present our results in narrative style. Ethics and dissemination This systematic review will not require any ethics approval since it only involves scientific articles. The review will be disseminated in a peer-reviewed journal and at various conferences fitting its scope
- ItemProjected early spread of COVID-19 in Africa(2020) Pearson, Carl A. B.; Van Schalkwyk, Cari; Foss, Anna M.; O'Reilly, Kathleen M.; CMMID COVID-19 working group; SACEMA; Pulliam, Juliet R. C.For African countries currently reporting COVID-19 cases, we estimate when they will report more than 1 000 and 10 000 cases. Assuming current trends, more than 80% are likely to exceed 1 000 cases by the end of April 2020, with most exceeding 10 000 a few weeks later.
- ItemThe role of remdesivir in South Africa : preventing COVID-19 deaths through increasing intensive care unit capacity(Oxford University Press, 2021-05) Nichols, Brooke E.; Jamieson, Lise; Zhang, Sabrina R. C.; Rao, Gabriella A.; Silal, Sheetal; Pulliam, Juliet R. C.; Sanne, Ian; Meyer-Rath, GesineCountries such as South Africa have limited intensive care unit (ICU) capacity to handle the expected number of patients with COVID-19 requiring ICU care. Remdesivir can prevent deaths in countries such as South Africa by decreasing the number of days people spend in ICU, therefore freeing up ICU bed capacity.
- ItemTransmission of Nipah virus — 14 years of investigations in Bangladesh(Massachusetts Medical Society, 2019-05-09) Nikolay, Birgit; Salje, Henrik; Hossain, Jahangir; Khan, Dawlat; Sazzad, Hossain M. S.; Rahman, Mahmudur; Daszak, Peter; Stroher, Ute; Pulliam, Juliet R. C.; Kilpatrick, Marm; Nichol, Stuart T.; Klena, John D.; Sultana, Sharmin; Afroj, Sayma; Luby, Stephen P.; Cauchemez, Simon; Gurley, Emily S.BACKGROUND: Nipah virus is a highly virulent zoonotic pathogen that can be transmitted between humans. Understanding the dynamics of person-to-person transmission is key to designing effective interventions. METHODS: We used data from all Nipah virus cases identified during outbreak investigations in Bangladesh from April 2001 through April 2014 to investigate case-patient characteristics associated with onward transmission and factors associated with the risk of infection among patient contacts. RESULTS: Of 248 Nipah virus cases identified, 82 were caused by person-to-person transmission, corresponding to a reproduction number (i.e., the average number of secondary cases per case patient) of 0.33 (95% confidence interval [CI], 0.19 to 0.59). The predicted reproduction number increased with the case patient’s age and was highest among patients 45 years of age or older who had difficulty breathing (1.1; 95% CI, 0.4 to 3.2). Case patients who did not have difficulty breathing infected 0.05 times as many contacts (95% CI, 0.01 to 0.3) as other case patients did. Serologic testing of 1863 asymptomatic contacts revealed no infections. Spouses of case patients were more often infected (8 of 56 [14%]) than other close family members (7 of 547 [1.3%]) or other contacts (18 of 1996 [0.9%]). The risk of infection increased with increased duration of exposure of the contacts (adjusted odds ratio for exposure of >48 hours vs. ≤1 hour, 13; 95% CI, 2.6 to 62) and with exposure to body fluids (adjusted odds ratio, 4.3; 95% CI, 1.6 to 11). CONCLUSIONS: Increasing age and respiratory symptoms were indicators of infectivity of Nipah virus. Interventions to control person-to-person transmission should aim to reduce exposure to body fluids. (Funded by the National Institutes of Health and others.)
- ItemUnderstanding and acting on the developmental origins of health and disease in Africa would improve health across generations(Taylor & Francis Open, 2017) Norris, Shane A.; Daar, Abdallah; Balasubramanian, Dorairajan; Byass, Peter; Kimani-Murage, Elizabeth; Macnab, Andrew; Pauw, Christoff; Singhal, Atul; Yajnik, Chittaranjan; Akazili, James; Levitt, Naomi; Maatoug, Jihene; Mkhwanazi, Nolwazi; Moore, Sophie E.; Nyirenda, Moffat; Pulliam, Juliet R. C.; Rochat, Tamsen; Said-Mohamed, Rihlat; Seedat, Soraya; Sobngwi, Eugene; Tomlinson, Mark; Toska, Elona; Van Schalkwyk, CariData from many high- and low- or middle-income countries have linked exposures during key developmental periods (in particular pregnancy and infancy) to later health and disease. Africa faces substantial challenges with persisting infectious disease and now burgeoning non-communicable disease.This paper opens the debate to the value of strengthening the developmental origins of health and disease (DOHaD) research focus in Africa to tackle critical public health challenges across the life-course. We argue that the application of DOHaD science in Africa to advance life-course prevention programmes can aid the achievement of the Sustainable Development Goals, and assist in improving health across generations. To increase DOHaD research and its application in Africa, we need to mobilise multisectoral partners, utilise existing data and expertise on the continent, and foster a new generation of young African scientists engrossed in DOHaD.