Productivity of mother pigs is lower, and mortality greater, in countries that still confine them in gestation crates.

Background: For decades, pig farmers have used gestation crates - small metal enclosures about two feet wide - to confine pregnant sows (female breeding pigs). Gestation crates physically restrain sows for most of their life, preventing them from walking or even turning around. Millions of females are still housed in these systems. Growing societal concern about animal welfare has been pressuring the industry for change, with recent legislation in the European Union and California restricting the use of crates. Still, the notion that gestation crates negatively affect sow welfare has been challenged by producers in regions where crates are widely used, who argue that, by facilitating health monitoring and preventing aggression, crates lead to lower sow mortality and higher piglet outputs per sow. We address these claims by comparing sow mortality and performance across countries with different housing systems. Methods: To this end, we use publicly available data from InterPig, a network of pig production economists in 17 countries that provides internationally harmonized methods for meaningful comparisons of national production data. Results: The results show that sow mortality is significantly higher, and annual pig production per sow significantly lower, in those countries where gestation crates are still the norm compared to countries in the European Union, where use of gestation crates is restricted to up to four weeks after insemination. Conclusions: Claims of higher mortality and reduced productivity per sow in crate-free systems are not substantiated by this data. This evidence should be considered in policies affecting the welfare of breeding pigs.

Pain-Track: a time-series approach for the description and analysis of the burden of pain.

OBJECTIVE: To present the Pain-Track, a novel framework for the description and analysis of the pain experience based on its temporal evolution, around which intensity and other attributes of pain (texture, anatomy), interventions and clinical symptoms can be registered. This time-series approach can provide valuable insight on the expected evolution of the pain typically associated with different medical conditions and on time-varying (risk) factors associated with the temporal dynamics of pain. RESULTS: We illustrate the use of the framework to explore hypotheses on the temporal profile of the pain associated with an acute injury (bone fracture), and the magnitude of the pain burden it represents. We also show that, by focusing on the critical dimensions of the pain experience (intensity and time), the approach can help map different conditions to a common scale directly relating to the experiences of those who endure them (time in pain), providing the basis for the quantification of the burden of pain inflicted upon individuals or populations. An electronic version for data entry and interpretation is also presented.

Laying hen mortality in different indoor housing systems: a meta-analysis of data from commercial farms in 16 countries.

Societal concern with the welfare of egg laying hens housed in conventional cages is fostering a transition towards cage-free systems in many countries. However, although cage-free facilities enable hens to move freely and express natural behaviours, concerns have also been raised over the possibility that cage-free flocks experience higher mortality, potentially compromising some aspects of their welfare. To investigate this possibility, we conducted a large meta-analysis of laying hen mortality in conventional cages, furnished cages and cage-free aviaries using data from 6040 commercial flocks and 176 million hens from 16 countries. We show that except for conventional cages, mortality gradually drops as experience with each system builds up: since 2000, each year of experience with cage-free aviaries was associated with a 0.35-0.65% average drop in cumulative mortality, with no differences in mortality between caged and cage-free systems in more recent years. As management knowledge evolves and genetics are optimized, new producers transitioning to cage-free housing may experience even faster rates of decline. Our results speak against the notion that mortality is inherently higher in cage-free production and illustrate the importance of considering the degree of maturity of production systems in any investigations of farm animal health, behaviour and welfare.

Respiratory syncytial virus causes more hospitalizations and deaths in equatorial Brazil than influenza (including during the 2009 pandemic).

Despite numerous studies evaluating influenza and Respiratory Syncytial Virus (RSV), there is still a lack of knowledge about them, especially in tropical countries. We compared the relative importance of respiratory viruses by examining their spatiotemporal patterns, age-specific hospitalization data and mortality data for 2007-2012 obtained from official sources. The data were aggregated into "respiratory infection seasonal zones" formed combining states that had similar seasonal patterns of pneumonia and influenza (P&I). Equatorial-North where P&I peaks in the middle of the year, Equatorial-South where P&I peaks in the first semester and coincides with the rainy-season, Subtropical where P&I peaks are clearly concentrated in the winter season, and Tropical Midwest and South-East where P&I peaks are a transition between the South-Equatorial and the Sub-tropical. Our analyses indicate that RSV has higher impact than influenza in equatorial region of Brazil, which was particularly evident during the circulation of the 2009pdm strain, and suggests that seasonal influenza may have a lower impact in Equatorial Brazil (and perhaps in other tropical regions of the world) than previously considered. Accordingly, we suggest that the broad assumption that influenza is the main cause of viral respiratory hospitalizations and death in equatorial regions be questioned with greater emphasis in future studies.

Comparison of malaria incidence rates and socioeconomic-environmental factors between the states of Acre and Rondônia: a spatio-temporal modelling study.

BACKGROUND: Plasmodium falciparum malaria is a threat to public health, but Plasmodium vivax malaria is most prevalent in Latin America, where the incidence rate has been increasing since 2016, particularly in Venezuela and Brazil. The Brazilian Amazon reported 193,000 cases in 2017, which were mostly confirmed as P. vivax (~ 90%). Herein, the relationships among malaria incidence rates and the proportion of accumulated deforestation were contrasted using data from the states of Acre and Rondônia in the south-western Brazilian Amazon. The main purpose is to test the hypothesis that the observed difference in incidence rates is associated with the proportion of accumulated deforestation. METHODS: An ecological study using spatial and temporal models for mapping and modelling malaria risk was performed. The municipalities of Acre and Rondônia were the spatial units of analysis, whereas month and year were the temporal units. The number of reported malaria cases from 2009 until 2015 were used to calculate the incidence rate per 1000 people at risk. Accumulated deforestation was calculated using publicly available satellite images. Geographically weighted regression was applied to provide a local model of the spatial heterogeneity of incidence rates. Time-series dynamic regression was applied to test the correlation of incidence rates and accumulated deforestation, adjusted by climate and socioeconomic factors. RESULTS: The malaria incidence rate declined in Rondônia but remained stable in Acre. There was a high and positive correlation between the decline in malaria and higher proportions of accumulated deforestation in Rondônia. Geographically weighted regression showed a complex relationship. As deforestation increased, malaria incidence also increased in Acre, while as deforestation increased, malaria incidence decreased in Rondônia. Time-series dynamic regression showed a positive association between malaria incidence and precipitation and accumulated deforestation, whereas the association was negative with the human development index in the westernmost areas of Acre. CONCLUSION: Landscape modification caused by accumulated deforestation is an important driver of malaria incidence in the Brazilian Amazon. However, this relationship is not linearly correlated because it depends on the overall proportion of the land covered by forest. For regions that are partially degraded, forest cover becomes a less representative component in the landscape, causing the abovementioned non-linear relationship. In such a scenario, accumulated deforestation can lead to a decline in malaria incidence.

Effect of pneumococcal conjugate vaccine introduction on childhood pneumonia mortality in Brazil: a retrospective observational study.

BACKGROUND: Understanding the real-world effect of pneumococcal conjugate vaccines (PCVs) on pneumonia mortality is crucial because of the expectation that increased PCV use will substantially reduce the burden of pneumonia deaths in children younger than 5 years. However, few post-vaccine introduction studies have estimated the benefits of PCV use on childhood mortality and results have been inconsistent. Therefore, we set out to assess the effect of introduction of ten-valent pneumococcal conjugate vaccine (PCV10) on pneumonia mortality in children in Brazil. METHODS: In this retrospective observational study, we used publicly available mortality data of children aged 3-59 months in Brazil. We separated data by age group (3-11 months, 3-23 months, and 3-59 months) and stratified data by three different socioeconomic factors of Brazilian municipalities (in 2010): Human Development Index, proportion of children living in extreme poverty, and proportion of mothers with no primary education. We first examined long-term trends in childhood pneumonia mortality in Brazil (from 1980 to 2014). We then assessed the effect of PCV10-introduced in Brazil in 2010-both nationally and in municipalities stratified by socioeconomic status, with a synthetic control approach as our primary analytical method. FINDINGS: Between 1980 and 2010, a period during which Brazil's Human Development Index rose substantially, national pneumonia mortality in children younger than 5 years decreased from about 150 to 15 deaths per 100 000 children younger than 5 years. Despite rapid uptake of PCV10 after its introduction in 2010, we observed a further vaccine-associated decline of about 10% in national childhood pneumonia mortality with our primary analytical method, with a high degree of uncertainty in the estimates. We observed larger reductions in municipal childhood pneumonia mortality in all three age groups (3-11 months, 3-23 months, and 3-59 months) in municipalities with a high percentage of extreme childhood poverty and mothers with no primary education, with the largest decrease observed in children aged 3-23 months in municipalities with low maternal education (24%, 95% credible interval 7-35). INTERPRETATION: The large reduction observed from 1980 to 2010 in national pneumonia mortality in children younger than 5 years underscores that improvements in nutrition, hygiene, education, and health care have an important role in reducing pneumonia mortality. Although the PCV-associated reduction in childhood pneumonia mortality at the national level was modest, we found that PCV led to larger reductions in low-income municipalities. Similarly, large benefits might occur when PCVs are introduced in other low-income settings. FUNDING: Bill & Melinda Gates Foundation and National Institute of Allergy and Infectious Diseases.

We could learn much more from 1918 pandemic-the (mis)fortune of research relying on original death certificates.

PURPOSE: The analysis of historical death certificates has enormous potential for understanding how the health of populations was shaped by diseases and epidemics and by the implementation of specific interventions. In Brazil, the systematic archiving of mortality records was initiated only in 1944-hence the analysis of death registers before this time requires searching for these documents in public archives, notaries, parishes, and especially ancient cemeteries, which are often the only remaining source of information about these deaths. This article describes an effort to locate original death certificates in Brazil and document their organization, accessibility, and preservation. METHODS: To this end, we conducted an exploratory study in 19 of the 27 Brazilian states, focusing on the period surrounding the 1918 influenza pandemic (1913-1921). We included 55 cemeteries, 22 civil archives, and one military archive. RESULTS: Apart from few exceptions, the results show the absence of a curatorial policy for the organization, access or even physical preservation of this material, frequently leading to unavailability, deterioration, and ultimately its complete loss. CONCLUSIONS: This study indicates the need to promote the preservation of a historical heritage that is a key to understanding historical epidemiological patterns and human responses to global health threats.

Rotavirus vaccination takes seasonal signature of childhood diarrhea back to pre-sanitation era in Brazil.

OBJECTIVES: This study aimed to examine the previously unknown long-term spatio-temporal patterns in diarrheal morbidity and mortality across age groups and geography in Brazil under the light of evolving socioeconomic factors and interventions. METHODS: Nationwide mortality (1979-2014) and hospitalization (1998-2014) data were obtained from the Brazilian Ministry of Health. Analyses of long-term secular trends and seasonality of diarrheal morbidity and mortality were performed in EPIPOI (www.epipoi.info). RESULTS: For most states, the primary peak in mortality risk among children under 5 years occurred from December-April (summer/early autumn) from 1979-1988. From 2000-2005 (before the 2006 implementation of rotavirus vaccination), the pattern switched to June-October (winter/early spring). By 2007-2014, the peak in mortality shifted back towards summer/early autumn. A similar pattern was observed for hospitalizations. These patterns were particularly apparent in non-equatorial regions of the country. In contrast, the risk of diarrhea-related death among older children (5-19 years) did not demonstrate well-defined seasonality or spatial patterns. CONCLUSIONS: Rotavirus vaccination policies were associated with a shift in the timing of seasonal peaks in children under 5, reminiscent of the summer diarrhea period common decades prior. Additionally, young children were shown to have distinct disease patterns compared to other age groups, suggesting different etiologies.

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 spatiotemporal characteristics of influenza A and B in the WHO European Region: can one define influenza transmission zones in Europe?

We aimed to assess the epidemiology and spatiotemporal patterns of influenza in the World Health Organization (WHO) European Region and evaluate the validity of partitioning the Region into five influenza transmission zones (ITZs) as proposed by the WHO. We used the FluNet database and included over 650,000 influenza cases from 2000 to 2015. We analysed the data by country and season (from July to the following June). We calculated the median proportion of cases caused by each virus type in a season, compared the timing of the primary peak between countries and used a range of cluster analysis methods to assess the degree of overlap between the WHO-defined and data-driven ITZs. Influenza A and B caused, respectively, a median of 83% and 17% cases in a season. There was a significant west-to-east and non-significant (p = 0.10) south-to-north gradient in the timing of influenza activity. Typically, influenza peaked in February and March; influenza A earlier than influenza B. Most countries in the WHO European Region would fit into two ITZs: 'Western Europe' and 'Eastern Europe'; countries bordering Asia may be better placed into extra-European ITZs. Our findings have implications for the presentation of surveillance data and prevention and control measures in this large WHO Region.

Influenza seasonality goes south in the Yucatan Peninsula: The case for a different influenza vaccine calendar in this Mexican region.

INTRODUCTION: While vaccination may be relatively straightforward for regions with a well-defined winter season, the situation is quite different for tropical regions. Influenza activity in tropical regions might be out of phase with the dynamics predicted for their hemispheric group thereby impacting the effectiveness of the immunization campaign. OBJECTIVE: To investigate how the climatic diversity of Mexico hinders its existing influenza immunization strategy and to suggest that the hemispheric vaccine recommendations be tailored to the regional level in order to optimize vaccine effectiveness. METHODS: We studied the seasonality of influenza throughoutMexico by modeling virological and mortality data.De-trended time series of each Mexican state were analyzed by Fourier decomposition to describe the amplitude and timing of annual influenza epidemic cycles and to compare with each the timing of the WHO's Northern and Southern Hemispheric vaccination schedule. FINDINGS: The timings of the primary (major) peaks of both virological and mortality data for most Mexican states are well aligned with the Northern Hemisphere winter (December-February) and vaccine schedule. However, influenza peaks in September in the three states of the Yucatan Peninsula. Influenza-related mortality also peaks in September in Quintana Roo and Yucatan whereas it peaks in May in Campeche. As the current timing of vaccination in Mexico is between October and November, more than half of the annual influenza cases have already occurred in the Yucatan Peninsula states by the time the Northern Hemispheric vaccine is delivered and administered. CONCLUSION: The current Northern Hemispheric influenza calendar adopted for Mexico is not optimal for the Yucatan Peninsula states thereby likely reducing the effectiveness of the immunization of the population. We recommend that Mexico tailor its immunization strategy to better reflect its climatologic and epidemiological diversity and adopt the WHO Southern Hemisphere influenza vaccine and schedule for the Yucatan Peninsula.

Characteristics of seasonal influenza A and B in Latin America: Influenza surveillance data from ten countries.

INTRODUCTION: The increased availability of influenza surveillance data in recent years justifies an actual and more complete overview of influenza epidemiology in Latin America. We compared the influenza surveillance systems and assessed the epidemiology of influenza A and B, including the spatio-temporal patterns of influenza epidemics, in ten countries and sub-national regions in Latin America. METHODS: We aggregated the data by year and country and characteristics of eighty-two years were analysed. We calculated the median proportion of laboratory-confirmed influenza cases caused by each virus strain, and compared the timing and amplitude of the primary and secondary peaks between countries. RESULTS: 37,087 influenza cases were reported during 2004-2012. Influenza A and B accounted for a median of 79% and, respectively, 21% of cases in a year. The percentage of influenza A cases that were subtyped was 82.5%; for influenza B, 15.6% of cases were characterized. Influenza A and B were dominant in seventy-five (91%) and seven (9%) years, respectively. In half (51%) of the influenza A years, influenza A(H3N2) was dominant, followed by influenza A(H1N1)pdm2009 (41%) and pre-pandemic A(H1N1) (8%). The primary peak of influenza activity was in June-September in temperate climate countries, with little or no secondary peak. Tropical climate countries had smaller primary peaks taking place in different months and frequently detectable secondary peaks. CONCLUSIONS: We found that good influenza surveillance data exists in Latin America, although improvements can still be made (e.g. a better characterization of influenza B specimens); that influenza B plays a considerable role in the seasonal influenza burden; and that there is substantial heterogeneity of spatio-temporal patterns of influenza epidemics. To improve the effectiveness of influenza control measures in Latin America, tropical climate countries may need to develop innovative prevention strategies specifically tailored to the spatio-temporal patterns of influenza in this region.

A global map of hemispheric influenza vaccine recommendations based on local patterns of viral circulation.

Both the Northern and the Southern Hemisphere annual WHO influenza vaccine recommendations are designed to ensure vaccine delivery before the winter-time peak of viral circulation in each hemisphere. However, influenza seasonal patterns are highly diverse in tropical countries and may be out of phase with the WHO recommendations for their respective hemisphere. We modelled the peak timing of influenza activity for 125 countries using laboratory-based surveillance data from the WHO's FLUNET database and compared it with the influenza hemispheric recommendations in place. Influenza vaccine recommendations for respectively 25% and 39% of the Northern and Southern Hemisphere countries were out of phase with peak influenza circulation in their corresponding hemisphere (62% and 53%, respectively, when the analysis was limited to the 52 countries in the tropical belt). These results indicate that routine influenza immunization efforts should be closely tailored to local patterns of viral circulation, rather than a country's hemispheric position.

Modeling the Impact of Alternative Immunization Strategies: Using Matrices as Memory Lanes.

Existing modeling approaches are divided between a focus on the constitutive (micro) elements of systems or on higher (macro) organization levels. Micro-level models enable consideration of individual histories and interactions, but can be unstable and subject to cumulative errors. Macro-level models focus on average population properties, but may hide relevant heterogeneity at the micro-scale. We present a framework that integrates both approaches through the use of temporally structured matrices that can take large numbers of variables into account. Matrices are composed of several bidimensional (time×age) grids, each representing a state (e.g. physiological, immunological, socio-demographic). Time and age are primary indices linking grids. These matrices preserve the entire history of all population strata and enable the use of historical events, parameters and states dynamically in the modeling process. This framework is applicable across fields, but particularly suitable to simulate the impact of alternative immunization policies. We demonstrate the framework by examining alternative strategies to accelerate measles elimination in 15 developing countries. The model recaptured long-endorsed policies in measles control, showing that where a single routine measles-containing vaccine is employed with low coverage, any improvement in coverage is more effective than a second dose. It also identified an opportunity to save thousands of lives in India at attractively low costs through the implementation of supplementary immunization campaigns. The flexibility of the approach presented enables estimating the effectiveness of different immunization policies in highly complex contexts involving multiple and historical influences from different hierarchical levels.

Environmental drivers of the spatiotemporal dynamics of respiratory syncytial virus in the United States.

Epidemics of respiratory syncytial virus (RSV) are known to occur in wintertime in temperate countries including the United States, but there is a limited understanding of the importance of climatic drivers in determining the seasonality of RSV. In the United States, RSV activity is highly spatially structured, with seasonal peaks beginning in Florida in November through December and ending in the upper Midwest in February-March, and prolonged disease activity in the southeastern US. Using data on both age-specific hospitalizations and laboratory reports of RSV in the US, and employing a combination of statistical and mechanistic epidemic modeling, we examined the association between environmental variables and state-specific measures of RSV seasonality. Temperature, vapor pressure, precipitation, and potential evapotranspiration (PET) were significantly associated with the timing of RSV activity across states in univariate exploratory analyses. The amplitude and timing of seasonality in the transmission rate was significantly correlated with seasonal fluctuations in PET, and negatively correlated with mean vapor pressure, minimum temperature, and precipitation. States with low mean vapor pressure and the largest seasonal variation in PET tended to experience biennial patterns of RSV activity, with alternating years of "early-big" and "late-small" epidemics. Our model for the transmission dynamics of RSV was able to replicate these biennial transitions at higher amplitudes of seasonality in the transmission rate. This successfully connects environmental drivers to the epidemic dynamics of RSV; however, it does not fully explain why RSV activity begins in Florida, one of the warmest states, when RSV is a winter-seasonal pathogen. Understanding and predicting the seasonality of RSV is essential in determining the optimal timing of immunoprophylaxis.

Evolution of bright colours in animals: worlds of prohibition and oblivion.

No evolutionary explanation for the striking colouration of coral reef fish has been established to date. Here I present the "Hyper-Visible World" hypothesis, which proposes that coral reef habitats impose special conditions on the evolution of body-colour communication for mobile fish - that is, fish that roam across coral reef formations. The special conditions are: 1) the high clarity of water during daylight hours, and 2) the unpredictable pattern/ visual complexity of the coral habitat itself. The hypothesis suggests that, in a signal transmission framework, the visual exposure (signal) of mobile fish cannot be effectively reduced so as to make a difference to predator-prey interactions. This negates the possibility of effective colour-based camouflage. In contrast, the selective pressures that usually come secondary to camouflage (such as sexual, aposematic or territorial display) benefit from these same conditions, driving the evolution of the colour patterns in this environment - the conspicuousness and dazzling colour diversity that we commonly associate with coral reef fish.

Characterization of regional influenza seasonality patterns in China and implications for vaccination strategies: spatio-temporal modeling of surveillance data.

BACKGROUND: The complexity of influenza seasonal patterns in the inter-tropical zone impedes the establishment of effective routine immunization programs. China is a climatologically and economically diverse country, which has yet to establish a national influenza vaccination program. Here we characterize the diversity of influenza seasonality in China and make recommendations to guide future vaccination programs. METHODS AND FINDINGS: We compiled weekly reports of laboratory-confirmed influenza A and B infections from sentinel hospitals in cities representing 30 Chinese provinces, 2005-2011, and data on population demographics, mobility patterns, socio-economic, and climate factors. We applied linear regression models with harmonic terms to estimate influenza seasonal characteristics, including the amplitude of annual and semi-annual periodicities, their ratio, and peak timing. Hierarchical Bayesian modeling and hierarchical clustering were used to identify predictors of influenza seasonal characteristics and define epidemiologically-relevant regions. The annual periodicity of influenza A epidemics increased with latitude (mean amplitude of annual cycle standardized by mean incidence, 140% [95% CI 128%-151%] in the north versus 37% [95% CI 27%-47%] in the south, p<0.0001). Epidemics peaked in January-February in Northern China (latitude ≥33°N) and April-June in southernmost regions (latitude <27°N). Provinces at intermediate latitudes experienced dominant semi-annual influenza A periodicity with peaks in January-February and June-August (periodicity ratio >0.6 in provinces located within 27.4°N-31.3°N, slope of latitudinal gradient with latitude -0.016 [95% CI -0.025 to -0.008], p<0.001). In contrast, influenza B activity predominated in colder months throughout most of China. Climate factors were the strongest predictors of influenza seasonality, including minimum temperature, hours of sunshine, and maximum rainfall. Our main study limitations include a short surveillance period and sparse influenza sampling in some of the southern provinces. CONCLUSIONS: Regional-specific influenza vaccination strategies would be optimal in China; in particular, annual campaigns should be initiated 4-6 months apart in Northern and Southern China. Influenza surveillance should be strengthened in mid-latitude provinces, given the complexity of seasonal patterns in this region. More broadly, our findings are consistent with the role of climatic factors on influenza transmission dynamics. Please see later in the article for the Editors' Summary.