Assessment of Survival Kinetics for Emergent Highly Pathogenic Clade 2.3.4.4 H5Nx Avian Influenza Viruses.

High pathogenicity avian influenza viruses (HPAIVs) cause high morbidity and mortality in poultry species. HPAIV prevalence means high numbers of infected wild birds could lead to spill over events for farmed poultry. How these pathogens survive in the environment is important for disease maintenance and potential dissemination. We evaluated the temperature-associated survival kinetics for five clade 2.3.4.4 H5Nx HPAIVs (UK field strains between 2014 and 2021) incubated at up to three temperatures for up to ten weeks. The selected temperatures represented northern European winter (4 °C) and summer (20 °C); and a southern European summer temperature (30 °C). For each clade 2.3.4.4 HPAIV, the time in days to reduce the viral infectivity by 90% at temperature T was established (DT), showing that a lower incubation temperature prolonged virus survival (stability), where DT ranged from days to weeks. The fastest loss of viral infectivity was observed at 30 °C. Extrapolation of the graphical DT plots to the x-axis intercept provided the corresponding time to extinction for viral decay. Statistical tests of the difference between the DT values and extinction times of each clade 2.3.4.4 strain at each temperature indicated that the majority displayed different survival kinetics from the other strains at 4 °C and 20 °C.

A Semiquantitative Scoring System for Histopathological and Immunohistochemical Assessment of Lesions and Tissue Tropism in Avian Influenza.

The main findings of the post-mortem examination of poultry infected with highly pathogenic avian influenza viruses (HPAIV) include necrotizing inflammation and viral antigen in multiple organs. The lesion profile displays marked variability, depending on viral subtype, strain, and host species. Therefore, in this study, a semiquantitative scoring system was developed to compare histopathological findings across a wide range of study conditions. Briefly, the severity of necrotizing lesions in brain, heart, lung, liver, kidney, pancreas, and/or lymphocytic depletion in the spleen is scored on an ordinal four-step scale (0 = unchanged, 1 = mild, 2 = moderate, 3 = severe), and the distribution of the viral antigen in parenchymal and endothelial cells is evaluated on a four-step scale (0 = none, 1 = focal, 2 = multifocal, 3 = diffuse). These scores are used for a meta-analysis of experimental infections with H7N7 and H5N8 (clade 2.3.4.4b) HPAIV in chickens, turkeys, and ducks. The meta-analysis highlights the rather unique endotheliotropism of these HPAIV in chickens and a more severe necrotizing encephalitis in H7N7-HPAIV-infected turkeys. In conclusion, the proposed scoring system can be used to condensate HPAIV-typical pathohistological findings into semiquantitative data, thus enabling systematic phenotyping of virus strains and their tissue tropism.

The impact of point-of-care testing for influenza A and B on patient flow and management in a medical assessment unit of a general hospital.

OBJECTIVES: Timely implementation of influenza infection control and treatment can significantly reduce the impact on Hospital resources and patient management when demand is at peak. Turnaround times of Laboratory based screening tests for the diagnosis of influenza may have an impact on the implementation of infection control measures and treatment. In this study the objectives included determining the correlation between the Abbott ID NOW point-of-care testing (POCT) instrument using the Influenza A&B2 test and the laboratory based GeneXpert Flu+RSV kit. In addition the impact of the POCT instrument on the prescription of antivirals and antibiotics was evaluated by comparing with practice when the instrument was not in place. RESULTS: The results of the correlation study with a cohort of 54 patients revealed the Abbott ID NOW POCT has 92% sensitivity for the detection of Influenza A, while specificity was 100% for both Influenza A and B. The impact of the POCT instrument on the frequency of prescription of antivirals and amount of antibiotics consumed (33% reduction in antibiotic consumption in a cohort of 65 (2017) and 61 (2018)) was significant. In addition the average patient length of Hospital stay was significantly reduced from 5.26 days to 3.73 days.

Risk factors and spatial relative risk assessment for influenza A virus in poultry and swine in backyard production systems of central Chile.

Backyard production systems (BPS) are a common form of poultry and swine production worldwide. The limited implementation of biosecurity standards in these operations makes BPS a potential source for the emergence of pathogens that have an impact on both animal and public health. Information regarding circulation of influenza A virus (IAV) in poultry and swine raised in BPS is scarce; particularly in South American countries. The objective of this study was to estimate prevalence and seroprevalence of IAV in BPS in central Chile, identify subtype diversity, evaluate risk factors and spatial relative risk for IAV. Samples were collected from 329 BPS from central Chile. Seroprevalence at BPS level was 34.7% (95% CI: 23.1%-46.2%), 19.7% (95% CI: 9.9%-30.6%) and 11.7% (95% CI: 7.2%-16.4%), whereas prevalence at BPS level was 4.2% (95% CI: 0.0%-8.8%), 8.2% (95% CI: 0.8%-14.0%) and 9.2% (95% CI: 4.8%-13.1%), for the Metropolitan, Valparaiso and LGB O'Higgins regions, respectively. Spatial analysis revealed that central-western area of Metropolitan region and the southern province of Valparaiso region could be considered as high-risk areas for IAV (spatial relative risk = 2.2, p < .05). Logistic regression models identified the practice of breeding both poultry and pigs at the BPS as a risk factor (95% CI 1.06-3.75). From 75 IAV ELISA-positive sera, 20 chicken sera had haemagglutination inhibition titres ranging from 20 to 160, and of these, 11 had microneutralization titres ranging from 40 to 960 for one or more IAV subtypes. Identified subtypes were H1, H3, H4, H9, H10 and H12. Results from this study highlight the need for further IAV surveillance programmes in BPS in Chile. Early detection of IAV strains circulating in backyard animals, especially in regions with large human populations, could have an enormous impact on animal and public health.

Improving risk assessment of the emergence of novel influenza A viruses by incorporating environmental surveillance.

Reassortment is an evolutionary mechanism by which influenza A viruses (IAV) generate genetic novelty. Reassortment is an important driver of host jumps and is widespread according to retrospective surveillance studies. However, predicting the epidemiological risk of reassortant emergence in novel hosts from surveillance data remains challenging. IAV strains persist and co-occur in the environment, promoting co-infection during environmental transmission. These conditions offer opportunity to understand reassortant emergence in reservoir and spillover hosts. Specifically, environmental RNA could provide rich information for understanding the evolutionary ecology of segmented viruses, and transform our ability to quantify epidemiological risk to spillover hosts. However, significant challenges with recovering and interpreting genomic RNA from the environment have impeded progress towards predicting reassortant emergence from environmental surveillance data. We discuss how the fields of genomics, experimental ecology and epidemiological modelling are well positioned to address these challenges. Coupling quantitative disease models and natural transmission studies with new molecular technologies, such as deep-mutational scanning and single-virus sequencing of environmental samples, should dramatically improve our understanding of viral co-occurrence and reassortment. We define observable risk metrics for emerging molecular technologies and propose a conceptual research framework for improving accuracy and efficiency of risk prediction. This article is part of the theme issue 'Dynamic and integrative approaches to understanding pathogen spillover'.

Analysis of influenza data generated by four epidemiological surveillance laboratories in Mexico, 2010-2016.

The disease caused by the influenza virus is a global public health problem due to its high rates of morbidity and mortality. Thus, analysis of the information generated by epidemiological surveillance systems has vital importance for health decision making. A retrospective analysis was performed using data generated by the four molecular diagnostic laboratories of the Mexican Social Security Institute between 2010 and 2016. Demographics, influenza positivity, seasonality, treatment choices and vaccination status analyses were performed for the vaccine according to its composition for each season. In all cases, both the different influenza subtypes and different age groups were considered separately. The circulation of A/H1N1pdm09 (48.7%), influenza A/H3N2 (21.1%), influenza B (12.6%), influenza A not subtyped (11%) and influenza A/H1N1 (6.6%) exhibited well-defined annual seasonality between November and March, and there were significant increases in the number of cases every 2 years. An inadequate use of oseltamivir was determined in 38% of cases, and the vaccination status in general varied between 12.1 and 18.5% depending on the season. Our results provide current information about influenza in Mexico and demonstrate the need to update both operational case definitions and medical practice guidelines to reduce the inappropriate use of antibiotics and antivirals.

Feedback Between Behavioral Adaptations and Disease Dynamics.

We study the feedback processes between individual behavior, disease prevalence, interventions and social networks during an influenza pandemic when a limited stockpile of antivirals is shared between the private and the public sectors. An economic model that uses prevalence-elastic demand for interventions is combined with a detailed social network and a disease propagation model to understand the feedback mechanism between epidemic dynamics, market behavior, individual perceptions, and the social network. An urban and a rural region are simulated to assess the robustness of results. Results show that an optimal split between the private and public sectors can be reached to contain the disease but the accessibility of antivirals from the private sector is skewed towards the richest income quartile. Also, larger allocations to the private sector result in wastage where individuals who do not need it are able to purchase it but who need it cannot afford it. Disease prevalence increases with household size and total contact time but not by degree in the social network, whereas wastage of antivirals decreases with degree and contact time. The best utilization of drugs is achieved when individuals with high contact time use them, who tend to be the school-aged children of large families.

Spotlight on avian pathology: red mite, a serious emergent problem in layer hens.

Dermanyssus gallinae, the poultry red mite, is currently the most important ectoparasite of the egg laying industry worldwide with an expanding global prevalence. As a blood-feeder, it causes anaemia and severe welfare issues to the hens and it is a major cause of economic losses. It is also a vector for Salmonella species, avian influenza and potentially for other vector-borne pathogens. Paradoxically, there is a notable lack of funding for research into poultry red mite and an urgent need for effective and safe control strategies, sustainable therapies, prophylactics and integrated pest management.

Assessment of autoregressive integrated moving average (ARIMA), generalized linear autoregressive moving average (GLARMA), and random forest (RF) time series regression models for predicting influenza A virus frequency in swine in Ontario, Canada.

Influenza A virus commonly circulating in swine (IAV-S) is characterized by large genetic and antigenic diversity and, thus, improvements in different aspects of IAV-S surveillance are needed to achieve desirable goals of surveillance such as to establish the capacity to forecast with the greatest accuracy the number of influenza cases likely to arise. Advancements in modeling approaches provide the opportunity to use different models for surveillance. However, in order to make improvements in surveillance, it is necessary to assess the predictive ability of such models. This study compares the sensitivity and predictive accuracy of the autoregressive integrated moving average (ARIMA) model, the generalized linear autoregressive moving average (GLARMA) model, and the random forest (RF) model with respect to the frequency of influenza A virus (IAV) in Ontario swine. Diagnostic data on IAV submissions in Ontario swine between 2007 and 2015 were obtained from the Animal Health Laboratory (University of Guelph, Guelph, ON, Canada). Each modeling approach was examined for predictive accuracy, evaluated by the root mean square error, the normalized root mean square error, and the model's ability to anticipate increases and decreases in disease frequency. Likewise, we verified the magnitude of improvement offered by the ARIMA, GLARMA and RF models over a seasonal-naïve method. Using the diagnostic submissions, the occurrence of seasonality and the long-term trend in IAV infections were also investigated. The RF model had the smallest root mean square error in the prospective analysis and tended to predict increases in the number of diagnostic submissions and positive virological submissions at weekly and monthly intervals with a higher degree of sensitivity than the ARIMA and GLARMA models. The number of weekly positive virological submissions is significantly higher in the fall calendar season compared to the summer calendar season. Positive counts at weekly and monthly intervals demonstrated a significant increasing trend. Overall, this study shows that the RF model offers enhanced prediction ability over the ARIMA and GLARMA time series models for predicting the frequency of IAV infections in diagnostic submissions.

Both hemispheric influenza vaccine recommendations would have missed near half of the circulating viruses in Madagascar.

BACKGROUND: Influenza immunization still poses a critical challenge globally and specifically for tropical regions due to their complex influenza circulation pattern. Tropical regions should select the WHO's Northern Hemisphere or Southern Hemisphere recommended vaccine composition based on local surveillance. Analyses of influenza immunization effectiveness have neglected to account for the proportion of circulating viruses prevented from causing infection each year. We investigate this question for Madagascar, where influenza vaccines are not widely available. METHODS: Seventy-eight Malagasy influenza strains characterized from 2002 to 2014 were challenged with hypothetical scenarios in which the WHO's Northern Hemisphere and Southern Hemisphere recommended vaccine compositions were provided to the population. Match between circulating and vaccine strains was determined by haemagglutination inhibition assays. Strain-specific positive matches were scored assuming 9 months of protection, and scenarios incorporated vaccine delays from zero to 5 months. RESULTS: Malagasy influenza strains matched 54% and 44%, respectively, with the Northern Hemisphere and Southern Hemisphere recommended vaccine strains when the vaccine was delivered as soon as available. The matching values further decreased when additional delivery and application delays were considered. Differences between recommended compositions were not statistically significant. CONCLUSION: Our results showed matching with the Northern Hemisphere vaccine barely above 50%, even in the more favourable scenario. This suggests that if implemented, routine influenza vaccines would not provide an optimal protection against half of the influenza strains circulating in any epidemic season of Madagascar. We suggest that this limitation in influenza vaccine efficacy deserves greater attention, and should be considered in cost/benefit analyses of national influenza immunization programmes.

The Mechanisms for Within-Host Influenza Virus Control Affect Model-Based Assessment and Prediction of Antiviral Treatment.

Models of within-host influenza viral dynamics have contributed to an improved understanding of viral dynamics and antiviral effects over the past decade. Existing models can be classified into two broad types based on the mechanism of viral control: models utilising target cell depletion to limit the progress of infection and models which rely on timely activation of innate and adaptive immune responses to control the infection. In this paper, we compare how two exemplar models based on these different mechanisms behave and investigate how the mechanistic difference affects the assessment and prediction of antiviral treatment. We find that the assumed mechanism for viral control strongly influences the predicted outcomes of treatment. Furthermore, we observe that for the target cell-limited model the assumed drug efficacy strongly influences the predicted treatment outcomes. The area under the viral load curve is identified as the most reliable predictor of drug efficacy, and is robust to model selection. Moreover, with support from previous clinical studies, we suggest that the target cell-limited model is more suitable for modelling in vitro assays or infection in some immunocompromised/immunosuppressed patients while the immune response model is preferred for predicting the infection/antiviral effect in immunocompetent animals/patients.

Risk Assessment of High Pathogenicity Avian Influenza Virus Introduction into Poland via Legal Importation of Live Poultry.

The risk of highly pathogenic avian influenza (HPAI) virus introduction via import of live poultry results from the probability that infected birds are exported from apparently HPAI-free areas during the silent phase of the epidemic, i.e., the period between an incursion of the virus into a susceptible population and a report on the outbreak by an exporting country. In our study we adapted a stochastic model, previously published in 2010 by Sánchez-Vizcaíno et al., with our own modifications in which the probability of HPAI introduction was assessed as the sum of the probabilities of entry of at least one infected bird from each susceptible species exported from each country into each Polish region (county). The mean annual probability of HPAI introduction into Poland via legal trade of live poultry was very low (3.07 × 10(-3), which corresponds to 1 outbreak every 326 yr). The highest risk was associated with the import of turkeys (62%) and chickens (33%). The exporting countries that contributed the most to the overall risk were Italy (31%), the Netherlands (24%), and the Czech Republic (17%). The risk was not evenly distributed across the country and it seemed higher in western, north-central, and eastern Poland while several counties of the north-west, central, or south-east parts of the country were at negligible risk. The applied model provides quantitative evidence that the risk of HPAI introduction through legal trade of poultry does not play a major role and that other paths, such as wild birds migrations or illegal trade, should be considered as the most-likely routes along which the virus can be introduced.

Assessment of the Potential Distance of Dispersal of High Pathogenicity Avian Influenza Virus by Wild Mallards.

This work presents the results of studies aimed at assessing the median and maximum distances covered by wild mallards (Anas platyrhynchos; n = 38), hypothetically infected with the high pathogenicity avian influenza virus (HPAIV) during spring migrations, using GPS-GSM tracking and published data on the susceptibility to HPAIV infection and duration of shedding. The model was based on the assumptions that the birds shed virus in the absence of clinical signs during infectious periods (IP) that were assumed to last 1 day (IP1), 4 days (IP4), and 8 days (IP8) and that each day of migration is a hypothetical day of the onset of IP. Using the haversine formula over a sliding timeframe corresponding to each IP, distances were estimated for each duck that undertook migration and then the maximum distance (Dmax) was selected. Ten mallards undertook spring migrations but, due to the loss of signal in the GPS-GSM devices, only three ducks were observed during autumn migrations. The following ranges of Dmax values were calculated for spring migrations: 124-382 km for IP1 (median 210 km), 208-632 km for IP4 (median 342 km), and 213-687 km for IP8 (median 370 km). The present study provides information that can be used as a data source to perform risk assessment related to the contribution of wild mallards in the dispersal of HPAIV over considerable distances.

An Assessment of the Expected Cost-Effectiveness of Quadrivalent Influenza Vaccines in Ontario, Canada Using a Static Model.

Ontario, Canada, immunizes against influenza using a trivalent inactivated influenza vaccine (IIV3) under a Universal Influenza Immunization Program (UIIP). The UIIP offers IIV3 free-of-charge to all Ontarians over 6 months of age. A newly approved quadrivalent inactivated influenza vaccine (IIV4) offers wider protection against influenza B disease. We explored the expected cost-utility and budget impact of replacing IIV3 with IIV4, within the context of Ontario's UIIP, using a probabilistic and static cost-utility model. Wherever possible, epidemiological and cost data were obtained from Ontario sources. Canadian or U.S. sources were used when Ontario data were not available. Vaccine efficacy for IIV3 was obtained from the literature. IIV4 efficacy was derived from meta-analysis of strain-specific vaccine efficacy. Conservatively, herd protection was not considered. In the base case, we used IIV3 and IIV4 prices of $5.5/dose and $7/dose, respectively. We conducted a sensitivity analysis on the price of IIV4, as well as standard univariate and multivariate statistical uncertainty analyses. Over a typical influenza season, relative to IIV3, IIV4 is expected to avert an additional 2,516 influenza cases, 1,683 influenza-associated medical visits, 27 influenza-associated hospitalizations, and 5 influenza-associated deaths. From a societal perspective, IIV4 would generate 76 more Quality Adjusted Life Years (QALYs) and a net societal budget impact of $4,784,112. The incremental cost effectiveness ratio for this comparison was $63,773/QALY. IIV4 remains cost-effective up to a 53% price premium over IIV3. A probabilistic sensitivity analysis showed that IIV4 was cost-effective with a probability of 65% for a threshold of $100,000/QALY gained. IIV4 is expected to achieve reductions in influenza-related morbidity and mortality compared to IIV3. Despite not accounting for herd protection, IIV4 is still expected to be a cost-effective alternative to IIV3 up to a price premium of 53%. Our conclusions were robust in the face of sensitivity analyses.

Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets.

After their disappearance from the human population in 1968, influenza H2 viruses have continued to circulate in the natural avian reservoir. The isolation of this virus subtype from multiple bird species as well as swine highlights the need to better understand the potential of these viruses to spread and cause disease in humans. Here we analyzed the virulence, transmissibility and receptor-binding preference of two avian influenza H2 viruses (H2N2 and H2N3) and compared them to a swine H2N3 (A/swine/Missouri/2124514/2006 [swMO]), and a human H2N2 (A/England/10/1967 [Eng/67]) virus using the ferret model as a mammalian host. Both avian H2 viruses possessed the capacity to spread efficiently between cohoused ferrets, and the swine (swMO) and human (Eng/67) viruses transmitted to naïve ferrets by respiratory droplets. Further characterization of the swMO hemagglutinin (HA) by x-ray crystallography and glycan microarray array identified receptor-specific adaptive mutations. As influenza virus quasispecies dynamics during transmission have not been well characterized, we sequenced nasal washes collected during transmission studies to better understand experimental adaptation of H2 HA. The avian H2 viruses isolated from ferret nasal washes contained mutations in the HA1, including a Gln226Leu substitution, which is a mutation associated with α2,6 sialic acid (human-like) binding preference. These results suggest that the molecular structure of HA in viruses of the H2 subtype continue to have the potential to adapt to a mammalian host and become transmissible, after acquiring additional genetic markers.

Relating influenza virus membrane fusion kinetics to stoichiometry of neutralizing antibodies at the single-particle level.

The ability of antibodies binding the influenza hemagglutinin (HA) protein to neutralize viral infectivity is of key importance in the design of next-generation vaccines and for prophylactic and therapeutic use. The two antibodies CR6261 and CR8020 have recently been shown to efficiently neutralize influenza A infection by binding to and inhibiting the influenza A HA protein that is responsible for membrane fusion in the early steps of viral infection. Here, we use single-particle fluorescence microscopy to correlate the number of antibodies or antibody fragments (Fab) bound to an individual virion with the capacity of the same virus particle to undergo membrane fusion. To this end, individual, infectious virus particles bound by fluorescently labeled antibodies/Fab are visualized as they fuse to a planar, supported lipid bilayer. The fluorescence intensity arising from the virus-bound antibodies/Fab is used to determine the number of molecules attached to viral HA while a fluorescent marker in the viral membrane is used to simultaneously obtain kinetic information on the fusion process. We experimentally determine that the stoichiometry required for fusion inhibition by both antibody and Fab leaves large numbers of unbound HA epitopes on the viral surface. Kinetic measurements of the fusion process reveal that those few particles capable of fusion at high antibody/Fab coverage display significantly slower hemifusion kinetics. Overall, our results support a membrane fusion mechanism requiring the stochastic, coordinated action of multiple HA trimers and a model of fusion inhibition by stem-binding antibodies through disruption of this coordinated action.

Pandemic preparedness and the Influenza Risk Assessment Tool (IRAT).

Influenza infections have resulted in millions of deaths and untold millions of illnesses throughout history. Influenza vaccines are the cornerstone of influenza prevention and control. Recommendations are made by the World Health Organization (WHO) 6-9 months in advance of the influenza season regarding what changes, if any, should be made in the formulation of seasonal influenza vaccines. This allows time to manufacture, test, distribute, and administer vaccine prior to the beginning of the influenza season. At the same time experts also consider which viruses not currently circulating in the human population, but with pandemic potential, pose the greatest risk to public health. Experts may conclude that one or more of these viruses are of enough concern to warrant development of a high-growth reassortant candidate vaccine virus. Subsequently, national authorities may determine that a vaccine should be manufactured, tested in clinical trials, and even stockpiled in some circumstances. The Influenza Risk Assessment Tool (IRAT) was created in an effort to develop a standardized set of elements that could be applied for decision making when evaluating pre-pandemic viruses. The tool is a simple, additive model, based on multi-attribute decision analysis . The ultimate goal is to identify an appropriate candidate vaccine virus and prepare a human vaccine before the virus adapts to infect and efficiently transmit in susceptible human populations. This pre-pandemic preparation allows production of vaccine-a strategy that could save lives and mitigate illness during a pandemic.

The development of poultry farms risk assessment tool for avian influenza in Imo State, Nigeria.

This study validated the content of a questionnaire that will be used for risk stratification in poultry farms in Imo State, Nigeria. The questionnaire was developed from avian influenza risk domains peculiar to poultry farms in Nigeria. The questionnaire was verified and modified by a group of five experts with research interest in Nigeria's poultry industry and avian influenza prevention. The questionnaire was distributed to 30 poultry farms selected from Imo State, Nigeria. The same poultry farms were visited one week after they completed the questionnaires for on-site observation. Agreement between survey and observation results was analyzed using the kappa statistic and rated as poor, fair, moderate, substantial, or nearly perfect; internal consistency of the survey was also computed. The mean kappa statistic for agreement between the survey and observations (validation) ranged from 0.06 to 1, poor to nearly perfect agreement. Eight questions showed poor agreement, four had a fair agreement, two items had moderate agreement, nineteen survey questions had substantial agreement and ten questions had nearly perfect agreement. Out of the 43 items in the questionnaire, 32 items were considered validated with coefficient alpha >0.70.

Antineuronal antibodies and infectious pathogens in severe acute pediatric encephalitis.

The pathogenesis of acute encephalitis is divided into either direct infection or by immune-mediated inflammation, but the cause is still unknown. This retrospective study aimed to screen antineuronal antibodies in children with severe acute encephalitis. Thirty-four children (22 boys and 12 girls) underwent assessments such as antineuronal antibodies survey for autoimmune encephalitis and polymerase chain reaction/viral culture and antibody assays for all commonly recognized causes of infectious encephalitis. Sixteen (47.1%) were positive for autoantibodies, including antiglutamic acid decarboxylase antibodies in 16 and voltage-gated potassium channel complex antibodies in 1. Sixteen patients (47.1%) had presumed infectious etiologies, including 6 with influenza, 6 with Mycoplasma pneumoniae, 3 with enterovirus, and 1 with herpes simplex virus. In this study, influenza and Mycoplasma pneumoniae infection are the main presumed causes of severe acute encephalitis in children, although an immune-mediated mechanism may also play a role.

Mass trees: a new phylogenetic approach and algorithm to chart evolutionary history with mass spectrometry.

A new phylogenetics approach and algorithm with which to chart the evolutionary history of organisms is presented. It utilizes mass spectral data produced from the proteolytic digestion of proteins, rather than partial or complete gene or translated gene sequences. The concept and validity of the approach is demonstrated herein using both theoretical and experimental mass data, together with the translated gene sequences of the hemagglutinin protein of the influenza virus. A comparison of the mass trees with conventional sequenced-based phylogenetic trees, using two separate tree comparison algorithms, reveals a high degree of similarity and congruence among the trees. Given that the mass map data can be generated more rapidly than gene sequences, even when next generation parallel sequencing is employed, mass trees offer new opportunities and advantages for phylogenetic analysis.