Assessing biases in phylodynamic inferences in the presence of super-spreaders

AbstractPhylodynamic analyses using pathogen genetic data have become popular for making epidemiological inferences. However, many methods assume that the underlying host population follows homogenous mixing patterns. Nevertheless, in real disease outbreaks, a small number of individuals infect a disproportionately large number of others (super-spreaders). Our objective was to quantify the degree of bias in estimating the epidemic starting date in the presence of super-spreaders using different sample selection strategies. We simulated 100 epidemics of a hypothetical pathogen (fast evolving foot and mouth disease virus-like) over a real livestock movement network allowing the genetic mutations in pathogen sequence. Genetic sequences were sampled serially over the epidemic, which were then used to estimate the epidemic starting date using Extended Bayesian Coalescent Skyline plot (EBSP) and Birth –death skyline plot (BDSKY) models. Our results showed that the degree of bias varies over different epidemic situations, with substantial overestimations on the epidemic duration occurring in some occasions. While the accuracy and precision of BDSKY were deteriorated when a super-spreader generat ed a larger proportion of secondary cases, those of EBSP were deteriorated when epidemics were shorter. The accuracies of the inference were similar irrespective of whether the analysis used all sampled sequences or only a subset of them, although the former required substantially long...
Source: Veterinary Research - Category: Veterinary Research Source Type: research

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Authors: Bleibtreu A, Bertine M, Bertin C, Houhou-Fidouh N, Visseaux B Abstract Since the first case of human infection by the Middle East respiratory syndrome coronavirus (MERS-CoV) in Saudi Arabia in June 2012, more than 2260 cases of confirmed MERS-CoV infection and 803 related deaths have been reported since the 16th of October 2018. The vast majority of these cases (71%) were reported in Saudi Arabia but the epidemic has now spread to 27 countries and has not ceased 6 years later, unlike SARS-CoV that disappeared a little less than 2 years after emerging. Due to the high fatality rate ...
Source: Medecine et Maladies Infectieuses - Category: Infectious Diseases Tags: Med Mal Infect Source Type: research
This article analyzes current issues related to maternal vaccination with a focus on emerging and epidemic viral infections and human rights.Recent FindingsHistorically, pregnant women have not been considered in the development of vaccines and have been excluded from participating in clinical trials and vaccination campaigns. Because of risk for injury and death of mothers and fetuses/infants during infectious disease outbreaks, it is important to consider their rights to receive any potential form of prevention or therapy available to non-pregnant individuals in order to enhance their well-being.SummaryIt is unacceptable...
Source: Current Tropical Medicine Reports - Category: Tropical Medicine Source Type: research
ConclusionsOur results reaffirm the high clinical and epidemiological impact of the epidemic outbreak in Cantabria and emphasises the need for optimising the current prevention measures against hepatitis A.ResumenAntecedentes y objetivos: Desde junio de 2016 se han producido brotes de hepatitis A en diversos países europeos, afectando principalmente a hombres que tienen sexo con hombres (HSH). El objetivo del presente trabajo fue valorar su impacto clínico y epidemiológico en Cantabria.Materiales y métodosSe recogieron retrospectivamente todos los casos de hepatitis A diagnosticados en Cantabria...
Source: Revista Clinica Espanola - Category: Internal Medicine Source Type: research
Publication date: Available online 10 November 2019Source: EpidemicsAuthor(s): Lee Worden, Sarah F. Ackley, Jennifer Zipprich, Kathleen Harriman, Wayne T.A. Enanoria, Rae Wannier, Travis C. PorcoAbstractA large measles outbreak in 2014–2015, linked to Disneyland theme parks, attracted international attention, and led to changes in California vaccine policy. We use dates of symptom onset and known epidemic links for California cases in this outbreak to estimate time-varying transmission in the outbreak, and to estimate generation membership of cases probabilistically. We find that transmission declined significantly d...
Source: Epidemics - Category: Epidemiology Source Type: research
[WHO] Abuja -In the short time it has existed, Nigeria's public health institute, the Nigeria Centre for Disease Control (NCDC), has reported, averted and controlled a myriad of disease outbreaks. A key factor in preventing either the occurrence or the spread of these outbreaks has been their early detection.
Source: AllAfrica News: Health and Medicine - Category: African Health Source Type: news
An eight-month-old boy is examined by a doctor in Dar es Salaam, Tanzania. Credit: Kristin Palitza/IPS By Ifeanyi NsoforABUJA, Nov 7 2019 (IPS) Free movement of people and goods across Africa increases the risk of transmission of infectious diseases. The continent must realise that it is no longer a question of if disease outbreaks will occur, but instead, of when, and how fast. The U.S. Centres for Disease Control says that within 36 hours, a disease outbreak can spread from a remote village to major urban cities of the world. According to preventepidemics.org, a website which ranks countries’ levels of e...
Source: IPS Inter Press Service - Health - Category: International Medicine & Public Health Authors: Tags: Africa Headlines Health Poverty & SDGs Source Type: news
by V íctor Hugo Peña-García, Rebecca C. Christofferson Chikungunya virus (CHIKV) emerged in Colombia in 2014 into a population presumed fully susceptible. This resulted in a quick and intense spread across Colombia, resulting in an epidemic that affected an estimated 450,000 people. The reported Colombian cases accounted for over 49% of all the cases reported to the PAHO. Eco-environmental factors are known to be associated with the spread of arboviruses such as CHIKV, and likely contribute to the differences in transmission profiles that were observed across several municipalities. To determine the a...
Source: PLoS Neglected Tropical Diseases - Category: Tropical Medicine Authors: Source Type: research
Publication date: Available online 5 November 2019Source: EpidemicsAuthor(s): Iain S. Koolhof, Katherine B. Gibney, Silvana Bettiol, Michael Charleston, Anke Wiethoelter, Anna-Lena Arnold, Patricia T. Campbell, Peter J. Neville, Phyo. Aung, Tsubasa Shiga, Scott Carver, Simon M. FirestoneAbstractRoss River virus (RRV) is Australia’s most epidemiologically important mosquito-borne disease. During RRV epidemics in the State of Victoria (such as 2010/11 and 2016/17) notifications can account for up to 30% of national RRV notifications. However, little is known about factors which can forecast RRV transmission in Victoria...
Source: Epidemics - Category: Epidemiology Source Type: research
It’s been a rough fall for Juul. After weeks of intensifying scrutiny from federal regulators, resulting in plans to pull many of its products off the market entirely, the company was hit on Oct. 29 with an explosive lawsuit filed by a former financial executive at the company, who alleged that Juul knowingly sold at least a million contaminated mint-flavored nicotine pods earlier this year. The plaintiff, former senior vice president of global finance Siddharth Breja, claims he was wrongfully terminated for raising concerns about the sale of these pods. The claims, which Juul vigorously denied in a statement provide...
Source: TIME: Health - Category: Consumer Health News Authors: Tags: Uncategorized public health Source Type: news
This study describes the efforts and outcomes associated with the establishment of a clinical sample repository during the 2016 Zika virus epidemic. To overcome the challenge of limited access to clinical samples to support diagnostic test development, multiple US Department of Health and Human Services (HHS) agencies formed a partnership to create the HHS Zika Specimen Repository. In 2016-2017, the Biomedical Advanced Research and Development Authority and the Centers for Disease Control and Prevention collected patient specimens (4420 convalescent sera aliquots from 100 donors and 7171 plasma aliquots from 239 donors), c...
Source: Public Health Reports - Category: International Medicine & Public Health Tags: Public Health Rep Source Type: research
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