Localization, epidemic transitions, and unpredictability of multistrain epidemics with an underlying genotype network

Mathematical disease modelling has long operated under the assumption that any one infectious disease is caused by one transmissible pathogen spreading among a population. This paradigm has been useful in simplifying the biological reality of epidemics and has allowed the modelling community to focus on the complexity of other factors such as population structure and interventions. However, there is an increasing amount of evidence that the strain diversity of pathogens, and their interplay with the host immune system, can play a large role in shaping the dynamics of epidemics. Here, we introduce a disease model with an underlying genotype network to account for two important mechanisms. One, the disease can mutate along network pathways as it spreads in a host population. Two, the genotype network allows us to define a genetic distance across strains and therefore to model the transcendence of immunity often observed in real world pathogens. We study the emergence of epidemics in this model, through its epidemic phase transitions, and highlight the role of the genotype network in driving cyclicity of diseases, large scale fluctuations, sequential epidemic transitions, as well as localization around specific strains of the associated pathogen. More generally, our model illustrates the richness of behaviours that are possible even in well-mixed host populations once we consider strain diversity and go beyond the "one disease equals one pathogen" paradigm

Eimeria species occurrence varies between geographic regions and poultry production systems and may influence parasite genetic diversity

Coccidiosis is one of the biggest challenges faced by the global poultry industry. Recent studies have highlighted the ubiquitous distribution of all Eimeria species which can cause this disease in chickens, but intriguingly revealed a regional divide in genetic diversity and population structure for at least one species, Eimeria tenella. The drivers associated with such distinct geographic variation are unclear, but may impact on the occurrence and extent of resistance to anticoccidial drugs and future subunit vaccines. India is one of the largest poultry producers in the world and includes a transition between E. tenella populations defined by high and low genetic diversity. The aim of this study was to identify risk factors associated with the prevalence of Eimeria species defined by high and low pathogenicity in northern and southern states of India, and seek to understand factors which vary between the regions as possible drivers for differential genetic variation. Faecal samples and data relating to farm characteristics and management were collected from 107 farms from northern India and 133 farms from southern India. Faecal samples were analysed using microscopy and PCR to identify Eimeria occurrence. Multiple correspondence analysis was applied to transform correlated putative risk factors into a smaller number of synthetic uncorrelated factors. Hierarchical cluster analysis was used to identify poultry farm typologies, revealing three distinct clusters in the studied regions. The association between clusters and presence of Eimeria species was assessed by logistic regression. The study found that large-scale broiler farms in the north were at greatest risk of harbouring any Eimeria species and a larger proportion of such farms were positive for E. necatrix, the most pathogenic species. Comparison revealed a more even distribution for E. tenella across production systems in south India, but with a lower overall occurrence. Such a polarised region- and system-specific distribution may contribute to the different levels of genetic diversity observed previously in India and may influence parasite population structure across much of Asia and Africa. The findings of the study can be used to prioritise target farms to launch and optimise appropriate anticoccidial strategies for long-term control

A study of CP violation in B±→DK±B±→DK± and B±→Dπ±B±→Dπ± decays with D→KS0K±π∓ final states

A first study of CP violation in the decay modes B± → [K0S K ±π∓]Dh± and B± → [K0S K ∓π±]Dh±, where h labels a K or π meson and D labels a D0 or D0 meson, is performed. The analysis uses the LHCb data set collected in pp collisions, corresponding to an integrated luminosity of 3 fb−1. The analysis is sensitive to the CP-violating CKM phase γ through seven observables: one charge asymmetry in each of the four modes and three ratios of the charge-integrated yields. The results are consistent with measurements of γ using other decay modes

Measurement of the Bc +meson lifetime using Bc +→J/ψμ+νμX decays

The lifetime of the B+ c meson is measured using semileptonic decays having a J/ψ meson and a muon in the final state. The data, corresponding to an integrated luminosity of 2 fb-1, are collected by the LHCb detector in pp collisions at a centre-of-mass energy of 8 TeV. The measured lifetime is τ = 509 ± 8 ± 12 fs, where the first uncertainty is statistical and the second is systematic

Searches for Λ0b and Ξ0b decays to K0spπ- and K0spK- final states with first observation of the Λ0b → k0spπ- decay

A search for previously unobserved decays of beauty baryons to the final states K0 spπ- and K0 spK- is reported. The analysis is based on a data sample corresponding to an integrated luminosity of 1.0 fb- of pp collisions. The Λ0 b → ̄K pπ- decay is observed with a significance of 8.6σ, with branching fraction (Equation Presented), where the uncertainties are statistical, systematic, from the ratio of fragmentation fractions f Λ 0 b/fd, and from the branching fraction of the B0 → K0π+π - normalisation channel, respectively. A first measurement is made of the CP asymmetry, giving (Equation Presented). No significant signals are seen for Λ0 b → K0 spK - decays, Ξ0 b decays to both the K 0 spπ- and K0 spK - final states, and the Λ0 b → D- s(→ K0 sK-)p decay, and upper limits on their branching fractions are reported

Measurement of Υ production in pp collisions at √s = 2.76 TeV

The production of Υ(1S), Υ(2S) and Υ(3S) mesons decaying into the dimuon final state is studied with the LHCb detector using a data sample corresponding to an integrated luminosity of 3.3pb-1 collected in proton-proton collisions at a centre-of-mass energy of √s = 2.76 TeV. The differential production cross-sections times dimuon branching fractions are measured as functions of the Υ transverse momentum and rapidity, over the ranges pT < 15 GeV/c and 2.0 < y < 4.5. The total cross-sections in this kinematic region, assuming unpolarised production, are measured to be (Formula presented.) where the first uncertainty is statistical and the second systematic

Studies of beauty baryon decays to D0ph− and Λ+ch− final states

Decays of beauty baryons to the D0ph− and Λ+ch− final states (where h indicates a pion or a kaon) are studied using a data sample of pp collisions, corresponding to an integrated luminosity of 1.0  fb−1, collected by the LHCb detector. The Cabibbo-suppressed decays Λ0b→D0pK− and Λ0b→Λ+cK− are observed, and their branching fractions are measured with respect to the decays Λ0b→D0pπ− and Λ0b→Λ+cπ−. In addition, the first observation is reported of the decay of the neutral beauty-strange baryon Ξ0b to the D0pK− final state, and a measurement of the Ξ0b mass is performed. Evidence of the Ξ0b→Λ+cK− decay is also reported

Precision measurement of the ratio of the Λb0 to B-0 lifetimes

The LHCb measurement of the lifetime ratio of the Λb0 baryon to the B-0 meson is updated using data corresponding to an integrated luminosity of 3.0 fb-1 collected using 7 and 8 TeV centre-of-mass energy pp collisions at the LHC. The decay modes used are Λb0→J/ψpK- and B-0→J/ψπ+K-, where the π +K - mass is consistent with that of the K-*0(892) meson. The lifetime ratio is determined with unprecedented precision to be 0.974 ± 0.006 ± 0.004, where the first uncertainty is statistical and the second systematic. This result is in agreement with original theoretical predictions based on the heavy quark expansion. Using the current world average of the B-0 lifetime, the Λb0 lifetime is found to be 1.479 ± 0.009 ± 0.010ps

Measurement of resonant and CP components in B0s→J/ψπ+π− decays

Structure of the decay B̄s0→J/ψπ+π- is studied using data corresponding to 3fb-1 of integrated luminosity from pp collisions produced by the LHC and collected by the LHCb detector. Five interfering π+π- states are required to describe the decay: f0(980),f0(1500),f0(1790),f2(1270), and f2′(1525). An alternative model including these states and a nonresonant J/ψπ+π- component also provides a good description of the data. Based on the different transversity components measured for the spin-2 intermediate states, the final state is found to be compatible with being entirely CP odd. The CP-even part is found to be <2.3% at a 95% confidence level. The f0(500) state is not observed, allowing a limit to be set on the absolute value of the mixing angle with the f0(980) of <7.7° at a 90% confidence level, consistent with a tetraquark interpretation of the f0(980) substructure

Search for CP violation in the decay D+→π−π+π+

A search for CP violation in the phase space of the decay D+→π−π+π+ is reported using pp collision data, corresponding to an integrated luminosity of 1.0 fb−1, collected by the LHCb experiment at a centre-of-mass energy of 7 TeV. The Dalitz plot distributions for 3.1×106D+ and D− candidates are compared with binned and unbinned model-independent techniques. No evidence for CP violation is found