scholarly journals Characterising the epidemic spread of Influenza A/H3N2 within a city through phylogenetics

2020 ◽  
Author(s):  
Nicola F. Müller ◽  
Daniel Wüthrich ◽  
Nina Goldman ◽  
Nadine Sailer ◽  
Claudia Saalfrank ◽  
...  
Keyword(s):  
Patient Information ◽  
Respiratory Diseases ◽  
Influenza Season ◽  
Sequence Data ◽  
The Elderly ◽  
Influenza Viruses ◽  
Transmission Network ◽  
Genetic Sequence ◽  
School Aged Children ◽  
Local Spread

AbstractInfecting large portions of the global population, seasonal influenza is a major burden on societies around the globe. While the global source sink dynamics of the different seasonal influenza viruses have been studied intensively, it’s local spread remains less clear. In order to improve our understanding of how influenza is transmitted on a city scale, we collected an extremely densely sampled set of influenza sequences alongside patient metadata. To do so, we sequenced influenza viruses isolated from patients of two different hospitals, as well as private practitioners in Basel, Switzerland during the 2016/2017 influenza season. The genetic sequences reveal that repeated introductions into the city drove the influenza season. We then reconstruct how the effective reproduction number changed over the course of the season. We find trends in transmission dynamics correlated positively with trends in temperature, but not relative humidity nor school holidays. Alongside the genetic sequence data that allows us to see how individual cases are connected, we gathered patient information, such as the age or household status. Zooming into the local transmission outbreaks suggests that the elderly were to a large extent infected within their own transmission network, while school children likely drove the spread within the remaining transmission network. These patterns will be valuable to plan interventions combating the spread of respiratory diseases within cities given that similar patterns are observed for other influenza seasons and cities.Author summaryAs shown with the current SARS-CoV-2 pandemic, respiratory diseases can quickly spread around the globe. While it can be hugely important to understand how diseases spread around the globe, local spread is most often the main driver of novel infections of respiratory diseases such as SARS-CoV-2 or influenza. We here use genetic sequence data alongside patient information to better understand what the drives the local spread of influenza by looking at the 2016/2017 influenza season in Basel, Switzerland as an example. The genetic sequence data allows us to reconstruct the how the transmission dynamics changed over the course of the season, which we correlate to changes, but not humidity or school holidays. Additionally, the genetic sequence data allows us to see how individual cases are connected. Using patient information, such as age and household status our analyses suggest that the elderly mainly transmit within their own transmission network. Additionally, they suggest that school aged children, but not pre-school aged children are important drivers of the local spread of influenza.

scholarly journals Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics

2020 ◽  
Vol 16 (11) ◽  
pp. e1008984
Author(s):  
Nicola F. Müller ◽  
Daniel Wüthrich ◽  
Nina Goldman ◽  
Nadine Sailer ◽  
Claudia Saalfrank ◽  
...  
Keyword(s):  
Influenza A ◽  
Seasonal Influenza ◽  
Influenza Season ◽  
Sequence Data ◽  
The Elderly ◽  
Influenza Viruses ◽  
Transmission Network ◽  
School Closures ◽  
School Aged Children ◽  
Private Practitioners

Infecting large portions of the global population, seasonal influenza is a major burden on societies around the globe. While the global source sink dynamics of the different seasonal influenza viruses have been studied intensively, its local spread remains less clear. In order to improve our understanding of how influenza is transmitted on a city scale, we collected an extremely densely sampled set of influenza sequences alongside patient metadata. To do so, we sequenced influenza viruses isolated from patients of two different hospitals, as well as private practitioners in Basel, Switzerland during the 2016/2017 influenza season. The genetic sequences reveal that repeated introductions into the city drove the influenza season. We then reconstruct how the effective reproduction number changed over the course of the season. While we did not find that transmission dynamics in Basel correlate with humidity or school closures, we did find some evidence that it may positively correlated with temperature. Alongside the genetic sequence data that allows us to see how individual cases are connected, we gathered patient information, such as the age or household status. Zooming into the local transmission outbreaks suggests that the elderly were to a large extent infected within their own transmission network. In the remaining transmission network, our analyses suggest that school-aged children likely play a more central role than pre-school aged children. These patterns will be valuable to plan interventions combating the spread of respiratory diseases within cities given that similar patterns are observed for other influenza seasons and cities.

scholarly journals perfectphyloR: An R package for reconstructing perfect phylogenies

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Charith B. Karunarathna ◽  
Jinko Graham
Keyword(s):  
Binary Tree ◽  
Sequence Data ◽  
R Package ◽  
Binary Sequences ◽  
Ancestral Haplotype ◽  
Perfect Phylogeny ◽  
Nested Partitions ◽  
Genetic Sequence ◽  
Insight Into ◽  
Rooted Binary Tree

Abstract Background A perfect phylogeny is a rooted binary tree that recursively partitions sequences. The nested partitions of a perfect phylogeny provide insight into the pattern of ancestry of genetic sequence data. For example, sequences may cluster together in a partition indicating that they arise from a common ancestral haplotype. Results We present an R package to reconstruct the local perfect phylogenies underlying a sample of binary sequences. The package enables users to associate the reconstructed partitions with a user-defined partition. We describe and demonstrate the major functionality of the package. Conclusion The package should be of use to researchers seeking insight into the ancestral structure of their sequence data. The reconstructed partitions have many applications, including the mapping of trait-influencing variants.

scholarly journals Mortality Risk from Respiratory Diseases due to Non-Optimal Temperature among Brazilian Elderlies

2021 ◽  
Vol 18 (11) ◽  
pp. 5550
Author(s):  
Ludmilla da Silva Viana Jacobson ◽  
Beatriz Fátima Alves de Oliveira ◽  
Rochelle Schneider ◽  
Antonio Gasparrini ◽  
Sandra de Souza Hacon
Keyword(s):  
Time Series ◽  
Respiratory Diseases ◽  
Respiratory Health ◽  
The Elderly ◽  
Optimal Temperature ◽  
Average Temperature ◽  
Exposure Response ◽  
Mean Temperature ◽  
Risk Of Mortality ◽  
Exposure Variable

Over the past decade, Brazil has experienced and continues to be impacted by extreme climate events. This study aims to evaluate the association between daily average temperature and mortality from respiratory disease among Brazilian elderlies. A daily time-series study between 2000 and 2017 in 27 Brazilian cities was conducted. Data outcomes were daily counts of deaths due to respiratory diseases in the elderly aged 60 or more. The exposure variable was the daily mean temperature from Copernicus ERA5-Land reanalysis. The association was estimated from a two-stage time series analysis method. We also calculated deaths attributable to heat and cold. The pooled exposure–response curve presented a J-shaped format. The exposure to extreme heat increased the risk of mortality by 27% (95% CI: 15–39%), while the exposure to extreme cold increased the risk of mortality by 16% (95% CI: 8–24%). The heterogeneity between cities was explained by city-specific mean temperature and temperature range. The fractions of deaths attributable to cold and heat were 4.7% (95% CI: 2.94–6.17%) and 2.8% (95% CI: 1.45–3.95%), respectively. Our results show a significant impact of non-optimal temperature on the respiratory health of elderlies living in Brazil. It may support proactive action implementation in cities that have critical temperature variations.

scholarly journals Origin of the European avian-like swine influenza viruses

2014 ◽  
Vol 95 (11) ◽  
pp. 2372-2376 ◽  
Author(s):  
Andi Krumbholz ◽  
Jeannette Lange ◽  
Andreas Sauerbrei ◽  
Marco Groth ◽  
Matthias Platzer ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Swine Influenza ◽  
H1n1 Influenza ◽  
Molecular Data ◽  
Influenza Viruses ◽  
Time Resolved ◽  
Genotype Constellation ◽  
Tree Inference

The avian-like swine influenza viruses emerged in 1979 in Belgium and Germany. Thereafter, they spread through many European swine-producing countries, replaced the circulating classical swine H1N1 influenza viruses, and became endemic. Serological and subsequent molecular data indicated an avian source, but details remained obscure due to a lack of relevant avian influenza virus sequence data. Here, the origin of the European avian-like swine influenza viruses was analysed using a collection of 16 European swine H1N1 influenza viruses sampled in 1979–1981 in Germany, the Netherlands, Belgium, Italy and France, as well as several contemporaneous avian influenza viruses of various serotypes. The phylogenetic trees suggested a triple reassortant with a unique genotype constellation. Time-resolved maximum clade credibility trees indicated times to the most recent common ancestors of 34–46 years (before 2008) depending on the RNA segment and the method of tree inference.

scholarly journals Mortality due to respiratory diseases in the elderly after influenza vaccination campaigns in the Federal District, Brazil, 1996-2009

2013 ◽  
Vol 39 (2) ◽  
pp. 198-204 ◽  
Author(s):  
Francisca Magalhães Scoralick ◽  
Luciana Paganini Piazzolla ◽  
Liana Laura Pires ◽  
Cleudsom Neri ◽  
Wladimir Kummer de Paula
Keyword(s):  
Mortality Rate ◽  
Influenza Vaccination ◽  
Respiratory Diseases ◽  
Positive Impact ◽  
Vaccination Campaign ◽  
Age Groups ◽  
Federal District ◽  
The Elderly ◽  
Analysis Data ◽  
Proportional Mortality

OBJECTIVE: To compare mortality rates due to respiratory diseases among elderly individuals residing in the Federal District of Brasília, Brazil, prior to and after the implementation of a national influenza vaccination campaign. METHODS: This was an ecological time series analysis. Data regarding the population of individuals who were over 60 years of age between 1996 and 2009 were obtained from official databases. The variables of interest were the crude mortality rate (CMR), the mortality rate due to the respiratory disease (MRRD), and the proportional mortality ratio (PMR) for respiratory diseases. We performed a qualitative analysis of the data for the period prior to and after the implementation of the vaccination campaign (1996-1999 and 2000-2009, respectively). RESULTS: The CMR increased with advancing age. Over the course of the study period, we observed reductions in the CMR in all of the age brackets studied, particularly among those aged 80 years or older. Reductions in the MRRD were also found in all of the age groups, especially in those aged 80 years or older. In addition, there was a decrease in the PMR for respiratory diseases in all age groups throughout the study period. The most pronounced decrease in the PMR for respiratory diseases in the ≥ 70 year age bracket occurred in 2000 (immediately following the implementation of the national vaccination campaign); in 2001, that rate increased in all age groups, despite the greater adherence to the vaccination campaign in comparison with that recorded for 2000. CONCLUSIONS: Influenza vaccination appears to have a positive impact on the prevention of mortality due to respiratory diseases, particularly in the population aged 70 or over.

scholarly journals Improving pandemic influenza risk assessment

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Colin A Russell ◽  
Peter M Kasson ◽  
Ruben O Donis ◽  
Steven Riley ◽  
John Dunbar ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Pandemic Influenza ◽  
Influenza A ◽  
Sequence Data ◽  
Virus Genome ◽  
Influenza Viruses ◽  
Influenza Surveillance ◽  
Human Influenza ◽  
Influenza A Viruses ◽  
Virus Genotype

Assessing the pandemic risk posed by specific non-human influenza A viruses is an important goal in public health research. As influenza virus genome sequencing becomes cheaper, faster, and more readily available, the ability to predict pandemic potential from sequence data could transform pandemic influenza risk assessment capabilities. However, the complexities of the relationships between virus genotype and phenotype make such predictions extremely difficult. The integration of experimental work, computational tool development, and analysis of evolutionary pathways, together with refinements to influenza surveillance, has the potential to transform our ability to assess the risks posed to humans by non-human influenza viruses and lead to improved pandemic preparedness and response.

scholarly journals Detection of adamantane-sensitive influenza A(H3N2) viruses in Australia, 2017: a cause for hope?

2017 ◽  
Vol 22 (47) ◽  
Author(s):  
Aeron Hurt ◽  
Naomi Komadina ◽  
Yi-Mo Deng ◽  
Matthew Kaye ◽  
Sheena Sullivan ◽  
...  
Keyword(s):  
Influenza A ◽  
Influenza Season ◽  
Influenza Viruses ◽  
M2 Protein ◽  
H3n2 Influenza

For over a decade virtually all A(H3N2) influenza viruses have been resistant to the adamantane class of antivirals. However, during the 2017 influenza season in Australia, 15/461 (3.3%) adamantane-sensitive A(H3N2) viruses encoding serine at residue 31 of the M2 protein were detected, more than the total number identified globally during the last 6 years. A return to wide circulation of adamantane-sensitive A(H3N2) viruses would revive the option of using these drugs for treatment and prophylaxis.

scholarly journals Public health implications of influenza B outbreaks in closed settings in the United Kingdom in the 2007/08 influenza season

2008 ◽  
Vol 13 (38) ◽  
Author(s):  
P Mook ◽  
J Ellis ◽  
J M Watson ◽  
CI Thompson ◽  
M Zambon ◽  
...  
Keyword(s):  
Public Health ◽  
United Kingdom ◽  
Burden Of Disease ◽  
Influenza A ◽  
Health Management ◽  
Influenza Season ◽  
Influenza B ◽  
Influenza A Viruses ◽  
School Aged Children ◽  
The United Kingdom

Several influenza B outbreaks occurred in closed settings late in the 2007/08 influenza season (October to mid-May) in the United Kingdom (UK), with implications for public health management. Influenza B viruses usually circulate late in the season and cause a milder disease than influenza A viruses [1]. Epidemics of influenza B usually occur every two to three years with the burden of disease falling predominantly on school-aged children [2].

scholarly journals Cardiorespiratory disorders in preschool aged children associated with aerogenic impact of benzene, phenol and formaldehyde

2019 ◽  
Vol 95 (1) ◽  
pp. 70-74
Author(s):  
Olga A. Maklakova ◽  
S. L. Valina
Keyword(s):  
Qt Interval ◽  
Respiratory Diseases ◽  
Creatine Phosphokinase ◽  
Reference Group ◽  
Cell Activity ◽  
Glutathione S Transferase ◽  
Chronic Respiratory Diseases ◽  
School Aged Children ◽  
Proliferative Cell ◽  
Airway Conductance

There was performed an examination of 437 pre-school aged children living in the conditions of the pollution of atmospheric air with benzene, phenol andformaldehyde. Children with the elevated blood content of benzene, phenol andformaldehyde were detected to be diagnosed as having chronic respiratory diseases and asteno-neurotic syndrome by 3 and 1.3 times more often, respectively, in contrast to the reference group. Cardiorespiratory disorders in children with the elevated content of benzene, phenol and formaldehyde are manifested by restrictive and mixed disorders of airway conductance followed by the increase in markers of proliferative cell activity (CA-72-4 and M 20), changes in the electrophysiologicalprocesses in cardiac muscle pronounced by the decreased electric ventricular systole (QT interval) followed by the decline of the content in blood of glutathione-S-transferase, zAMF, nitrogen oxide and the increase in the lipids hydroperoxide level, and creatine phosphokinase activity.

scholarly journals Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses

2016 ◽  
Vol 113 (12) ◽  
pp. E1701-E1709 ◽  
Author(s):  
Richard A. Neher ◽  
Trevor Bedford ◽  
Rodney S. Daniels ◽  
Colin A. Russell ◽  
Boris I. Shraiman
Keyword(s):  
Influenza Virus ◽  
Seasonal Influenza ◽  
Sequence Data ◽  
Influenza Viruses ◽  
Surface Glycoprotein ◽  
Amino Acid Substitutions ◽  
Model Output ◽  
Virus Population ◽  
Web Browser ◽  
Antigenic Properties

Human seasonal influenza viruses evolve rapidly, enabling the virus population to evade immunity and reinfect previously infected individuals. Antigenic properties are largely determined by the surface glycoprotein hemagglutinin (HA), and amino acid substitutions at exposed epitope sites in HA mediate loss of recognition by antibodies. Here, we show that antigenic differences measured through serological assay data are well described by a sum of antigenic changes along the path connecting viruses in a phylogenetic tree. This mapping onto the tree allows prediction of antigenicity from HA sequence data alone. The mapping can further be used to make predictions about the makeup of the future A(H3N2) seasonal influenza virus population, and we compare predictions between models with serological and sequence data. To make timely model output readily available, we developed a web browser-based application that visualizes antigenic data on a continuously updated phylogeny.

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