Searching PubMed during a Pandemic

Background

The 2009 influenza A(H1N1) pandemic has generated thousands of articles and news items. However, finding relevant scientific articles in such rapidly developing health crises is a major challenge which, in turn, can affect decision-makers'' ability to utilise up-to-date findings and ultimately shape public health interventions. This study set out to show the impact that the inconsistent naming of the pandemic can have on retrieving relevant scientific articles in PubMed/MEDLINE.

Methodology

We first formulated a PubMed search algorithm covering different names of the influenza pandemic and simulated the results that it would have retrieved from weekly searches for relevant new records during the first 10 weeks of the pandemic. To assess the impact of failing to include every term in this search, we then conducted the same searches but omitted in turn “h1n1,” “swine,” “influenza” and “flu” from the search string, and compared the results to those for the full string.

Principal Findings

On average, our core search string identified 44.3 potentially relevant new records at the end of each week. Of these, we determined that an average of 27.8 records were relevant. When we excluded one term from the string, the percentage of records missed out of the total number of relevant records averaged 18.7% for omitting “h1n1,” 13.6% for “swine,” 17.5% for “influenza,” and 20.6% for “flu.”

Conclusions

Due to inconsistent naming, while searching for scientific material about rapidly evolving situations such as the influenza A(H1N1) pandemic, there is a risk that one will miss relevant articles. To address this problem, the international scientific community should agree on nomenclature and the specific name to be used earlier, and the National Library of Medicine in the US could index potentially relevant materials faster and allow publishers to add alert tags to such materials.     

Inter-Seasonal Influenza is Characterized by Extended Virus Transmission and Persistence

The factors that determine the characteristic seasonality of influenza remain enigmatic. Current models predict that occurrences of influenza outside the normal surveillance season within a temperate region largely reflect the importation of viruses from the alternate hemisphere or from equatorial regions in Asia. To help reveal the drivers of seasonality we investigated the origins and evolution of influenza viruses sampled during inter-seasonal periods in Australia. To this end we conducted an expansive phylogenetic analysis of 9912, 3804, and 3941 hemagglutinnin (HA) sequences from influenza A/H1N1pdm, A/H3N2, and B, respectively, collected globally during the period 2009-2014. Of the 1475 viruses sampled from Australia, 396 (26.8% of Australian, or 2.2% of global set) were sampled outside the monitored temperate influenza surveillance season (1 May – 31 October). Notably, rather than simply reflecting short-lived importations of virus from global localities with higher influenza prevalence, we documented a variety of more complex inter-seasonal transmission patterns including “stragglers” from the preceding season and “heralds” of the forthcoming season, and which included viruses sampled from clearly temperate regions within Australia. We also provide evidence for the persistence of influenza B virus between epidemic seasons, in which transmission of a viral lineage begins in one season and continues throughout the inter-seasonal period into the following season. Strikingly, a disproportionately high number of inter-seasonal influenza transmission events occurred in tropical and subtropical regions of Australia, providing further evidence that climate plays an important role in shaping patterns of influenza seasonality.     

National and Local Influenza Surveillance through Twitter: An Analysis of the 2012-2013 Influenza Epidemic

Social media have been proposed as a data source for influenza surveillance because they have the potential to offer real-time access to millions of short, geographically localized messages containing information regarding personal well-being. However, accuracy of social media surveillance systems declines with media attention because media attention increases “chatter” – messages that are about influenza but that do not pertain to an actual infection – masking signs of true influenza prevalence. This paper summarizes our recently developed influenza infection detection algorithm that automatically distinguishes relevant tweets from other chatter, and we describe our current influenza surveillance system which was actively deployed during the full 2012-2013 influenza season. Our objective was to analyze the performance of this system during the most recent 2012–2013 influenza season and to analyze the performance at multiple levels of geographic granularity, unlike past studies that focused on national or regional surveillance. Our system’s influenza prevalence estimates were strongly correlated with surveillance data from the Centers for Disease Control and Prevention for the United States (r = 0.93, p < 0.001) as well as surveillance data from the Department of Health and Mental Hygiene of New York City (r = 0.88, p < 0.001). Our system detected the weekly change in direction (increasing or decreasing) of influenza prevalence with 85% accuracy, a nearly twofold increase over a simpler model, demonstrating the utility of explicitly distinguishing infection tweets from other chatter.     

Gauging U.S. Emergency Medical Services Workers' Willingness to Respond to Pandemic Influenza Using a Threat- and Efficacy-Based Assessment Framework

Background

Emergency Medical Services workers'' willingness to report to duty in an influenza pandemic is essential to healthcare system surge amidst a global threat. Application of Witte''s Extended Parallel Process Model (EPPM) has shown utility for revealing influences of perceived threat and efficacy on non-EMS public health providers'' willingness to respond in an influenza pandemic. We thus propose using an EPPM-informed assessment of EMS workers'' perspectives toward fulfilling their influenza pandemic response roles.

Methodology/Principal Findings

We administered an EPPM-informed snapshot survey about attitudes and beliefs toward pandemic influenza response, to a nationally representative, stratified random sample of 1,537 U.S. EMS workers from May–June 2009 (overall response rate: 49%). Of the 586 respondents who met inclusion criteria (currently active EMS providers in primarily EMS response roles), 12% indicated they would not voluntarily report to duty in a pandemic influenza emergency if asked, 7% if required. A majority (52%) indicated their unwillingness to report to work if risk of disease transmission to family existed. Confidence in personal safety at work (OR = 3.3) and a high threat/high efficacy (“concerned and confident”) EPPM profile (OR = 4.7) distinguished those who were more likely to voluntarily report to duty. Although 96% of EMS workers indicated that they would probably or definitely report to work if they were guaranteed a pandemic influenza vaccine, only 59% had received an influenza immunization in the preceding 12 months.

Conclusions/Significance

EMS workers'' response willingness gaps pose a substantial challenge to prehospital surge capacity in an influenza pandemic. “Concerned and confident” EMS workers are more than four times as likely to fulfill pandemic influenza response expectations. Confidence in workplace safety is a positively influential modifier of their response willingness. These findings can inform insights into interventions for enhancing EMS workers'' willingness to respond in the face of a global infectious disease threat.     

Complete Genome Sequence of a Novel H4N1 Influenza Virus Isolated from a Pig in Central China

Pigs are proposed to be “mixing vessel” hosts that can produce genetically novel reassortant viruses with pandemic potential. The appearance of any novel influenza viruses among pigs should pose concerns for human health. Here, we report the complete genome sequence of a novel H4N1 influenza virus [A/Swine/HuBei/06/2009(H4N1)] isolated from a pig in Central China in 2009. The genomic sequence analysis indicates that this virus is a wholly avian-original influenza virus. Each gene may come from different avian influenza viruses outside mainland China, suggesting the role of migratory birds in the dispersal of influenza virus.     

Age-Specific Mortality During the 1918 Influenza Pandemic: Unravelling the Mystery of High Young Adult Mortality

The worldwide spread of a novel influenza A (H1N1) virus in 2009 showed that influenza remains a significant health threat, even for individuals in the prime of life. This paper focuses on the unusually high young adult mortality observed during the Spanish flu pandemic of 1918. Using historical records from Canada and the U.S., we report a peak of mortality at the exact age of 28 during the pandemic and argue that this increased mortality resulted from an early life exposure to influenza during the previous Russian flu pandemic of 1889–90. We posit that in specific instances, development of immunological memory to an influenza virus strain in early life may lead to a dysregulated immune response to antigenically novel strains encountered in later life, thereby increasing the risk of death. Exposure during critical periods of development could also create holes in the T cell repertoire and impair fetal maturation in general, thereby increasing mortality from infectious diseases later in life. Knowledge of the age-pattern of susceptibility to mortality from influenza could improve crisis management during future influenza pandemics.

“The war is over – and I must go” Egon Schiele, 1890–1918.

     

Prevention of influenza in the general population

Background

Although all jurisdictions in Canada offer annual influenza immunization to people at high risk of complications, only Ontario has provided universal annual immunization of healthy adults and children. Use of chemotherapy (amantidine, neuraminidase inhibitors) to prevent influenza varies among provinces. We sought to systematically review the evidence for the prevention of influenza infection in the general population.

Methods

The interventions reviewed were influenza vaccination and prophylactic use of neuraminidase inhibitors. The health outcomes of interest were rates of laboratory-confirmed influenza infection, clinical definitions of influenza-like illness and work absenteeism. MEDLINE and Cochrane databases were searched for relevant articles published between 1966 and March 2003. Only randomized controlled trials (RCTs) were selected. Evidence was appraised using the methodology of the Canadian Task Force on Preventive Health Care.

Results

Eighteen trials involving more than 33 000 healthy adults were identified that met the inclusion criteria; of these, 15 showed that influenza vaccination with either live-attenuated and inactivated vaccines was efficacious. Eleven trials were considered to be of “good” quality, and 7 were considered to be of “fair” quality. The relative risk reduction (RRR) associated with influenza immunization in adults ranged from 0% to 91%. Fifteen RCTs involving more than 45 000 healthy children aged 6 months to 19 years were identified, of which 9 were considered to contain “good” evidence and 6 “fair” evidence. Results from 12 of these trials showed protection against influenza. The RRR ranged from 0% to 93%. There were 6 RCTs of “good” quality showing that neuraminidase inhibitors are effective in preventing influenza infection. Side effects from both influenza vaccination and neuraminidase inhibitor administration were mild.

Interpretation

There are numerous RCTs of good quality in large populations that have consistently shown that influenza vaccination, using inactivated or live-attenuated vaccines, is moderately effective in preventing influenza in the general population (healthy adults and children over 6 months of age). There is good evidence that neuraminidase inhibitor prophylaxis in contacts given within 36 to 48 hours of symptom onset of the household index case is effective; appropriate use of this prevention method requires access to rapid diagnostic methods. Decisions about introduction of routine immunization programs must take into account the cost and cost-effectiveness of a universal program and the burden of illness associated with influenza in each jurisdiction.Influenza virus causes yearly epidemics of respiratory illness of varying severity worldwide in people of all ages, and it may be the most important cause of medically attended acute respiratory illness.¹ In Canada influenza and pneumonia are the leading cause of death from infection and the sixth cause of death overall.² Rates of complications and death from influenza are high among adults over 65 years of age and people with cardiac or pulmonary disease or chronic medical conditions, and annual influenza immunization in this population is associated with lower frequency of hospital admissions because of respiratory disease, congestive heart failure and death from any cause.^3,4 Previously healthy young children are increasingly recognized as having hospital admission rates comparable to those among elderly people during influenza epidemics⁵ and up to 12-fold greater than rates among older children.⁶ Because influenza occurs yearly and because re-infections occur throughout the lifespan and affect up to 20% of the population each year, considerable attention has been directed to the prevention of influenza in healthy people. Although annual immunization programs are routinely offered to high-risk groups, only the province of Ontario routinely offers influenza immunization to healthy adults and children.We performed a systematic review of the literature to answer the following question: how effective are the influenza vaccine and prophylactic neuraminidase inhibitor antiviral agents for the prevention of influenza in healthy adults and children?     

Examining Perceptions about Mandatory Influenza Vaccination of Healthcare Workers through Online Comments on News Stories

Background

The aim of this study was to understand online public perceptions of the debate surrounding the choice of annual influenza vaccinations or wearing masks as a condition of employment for healthcare workers, such as the one enacted in British Columbia in August 2012.

Methods

Four national and 82 local (British Columbia) Canadian online news sites were searched for articles posted between August 2012 and May 2013 containing the words “healthcare workers” and “mandatory influenza vaccinations/immunizations” or “mandatory flu shots and healthcare workers.” We included articles from sources that predominantly concerned our topic of interest and that generated reader comments. Two researchers coded the unedited comments using thematic analysis, categorizing codes to allow themes to emerge. In addition to themes, the comments were categorized by: 1) sentiment towards influenza vaccines; 2) support for mandatory vaccination policies; 3) citing of reference materials or statistics; 4) self-identified health-care worker status; and 5) sharing of a personal story.

Results

1163 comments made by 648 commenters responding to 36 articles were analyzed. Popular themes included concerns about freedom of choice, vaccine effectiveness, patient safety, and distrust in government, public health, and the pharmaceutical industry. Almost half (48%) of commenters expressed a negative sentiment toward the influenza vaccine, 28% were positive, 20% were neutral, and 4% expressed mixed sentiment. Of those who commented on the policy, 75% did not support the condition to work policy, while 25% were in favour. Of the commenters, 11% self-identified as healthcare workers, 13% shared personal stories, and 18% cited a reference or statistic.

Interpretation

The perception of the influenza vaccine in the comment sections of online news sites is fairly poor. Public health agencies should consider including online forums, comment sections, and social media sites as part of their communication channels to correct misinformation regarding the benefits of HCW influenza immunization and the effectiveness of the vaccine.     

Treating and Preventing Influenza in Aged Care Facilities: A Cluster Randomised Controlled Trial

Background

Influenza is an important cause of morbidity and mortality for frail older people. Whilst the antiviral drug oseltamivir (a neuraminidase inhibitor) is approved for treatment and prophylaxis of influenza during outbreaks, there have been no trials comparing treatment only (T) versus treatment and prophylaxis (T&P) in Aged Care Facilities (ACFs). Our objective was to compare a policy of T versus T&P for influenza outbreaks in ACFs.

Methods and Findings

We performed a cluster randomised controlled trial in 16 ACFs, that followed a policy of either “T”—oseltamivir treatment (75 mg twice a day for 5 days)—or “T&P”—treatment and prophylaxis (75 mg once a day for 10 days) for influenza outbreaks over three years, in addition to enhanced surveillance. The primary outcome measure was the attack rate of influenza. Secondary outcomes measures were deaths, hospitalisation, pneumonia and adverse events. Laboratory testing was performed to identify the viral cause of influenza-like illness (ILI) outbreaks. The study period 30 June 2006 to 23 December 2008 included three southern hemisphere winters. During that time, influenza was confirmed as the cause of nine of the 23 ILI outbreaks that occurred amongst the 16 ACFs. The policy of T&P resulted in a significant reduction in the influenza attack rate amongst residents: 93/255 (36%) in residents in T facilities versus 91/397 (23%) in T&P facilities (p = 0.002). We observed a non-significant reduction in staff: 46/216 (21%) in T facilities versus 47/350 (13%) in T&P facilities (p = 0.5). There was a significant reduction in mean duration of outbreaks (T = 24 days, T&P = 11 days, p = 0.04). Deaths, hospitalisations and pneumonia were non-significantly reduced in the T&P allocated facilities. Drug adverse events were common but tolerated.

Conclusion

Our trial lacked power but these results provide some support for a policy of “treatment and prophylaxis” with oseltamivir in controlling influenza outbreaks in ACFs.

Trail Registration

Australian Clinical Trials Registry ACTRN12606000278538     

Genome Wide Association Study Identifies New Loci Associated with Undesired Coat Color Phenotypes in Saanen Goats

This paper reports a quantitative genetics and genomic analysis of undesirable coat color patterns in goats. Two undesirable coat colors have routinely been recorded for the past 15 years in French Saanen goats. One fifth of Saanen females have been phenotyped “pink” (8.0%) or “pink neck” (11.5%) and consequently have not been included in the breeding program as elite animals. Heritability of the binary “pink” and “pink neck” phenotype, estimated from 103,443 females was 0.26 for “pink” and 0.21 for “pink neck”. Genome wide association studies (using haplotypes or single SNPs) were implemented using a daughter design of 810 Saanen goats sired by 9 Artificial Insemination bucks genotyped with the goatSNP50 chip. A highly significant signal (-log10pvalue = 10.2) was associated with the “pink neck” phenotype on chromosome 11, suggesting the presence of a major gene. Highly significant signals for the “pink” phenotype were found on chromosomes 5 and 13 (-log10p values of 7.2 and, 7.7 respectively). The most significant SNP on chromosome 13 was in the ASIP gene region, well known for its association with coat color phenotypes. Nine significant signals were also found for both traits. The highest signal for each trait was detected by both single SNP and haplotype approaches, whereas the smaller signals were not consistently detected by the two methods. Altogether these results demonstrated a strong genetic control of the “pink” and “pink neck” phenotypes in French Saanen goats suggesting that SNP information could be used to identify and remove undesired colored animals from the breeding program.     

Sound Symbolism in the Languages of Australia

The notion that linguistic forms and meanings are related only by convention and not by any direct relationship between sounds and semantic concepts is a foundational principle of modern linguistics. Though the principle generally holds across the lexicon, systematic exceptions have been identified. These “sound symbolic” forms have been identified in lexical items and linguistic processes in many individual languages. This paper examines sound symbolism in the languages of Australia. We conduct a statistical investigation of the evidence for several common patterns of sound symbolism, using data from a sample of 120 languages. The patterns examined here include the association of meanings denoting “smallness” or “nearness” with front vowels or palatal consonants, and the association of meanings denoting “largeness” or “distance” with back vowels or velar consonants. Our results provide evidence for the expected associations of vowels and consonants with meanings of “smallness” and “proximity” in Australian languages. However, the patterns uncovered in this region are more complicated than predicted. Several sound-meaning relationships are only significant for segments in prominent positions in the word, and the prevailing mapping between vowel quality and magnitude meaning cannot be characterized by a simple link between gradients of magnitude and vowel F2, contrary to the claims of previous studies.     

Using Extreme Value Theory Approaches to Forecast the Probability of Outbreak of Highly Pathogenic Influenza in Zhejiang,China

BackgroundInfluenza is a contagious disease with high transmissibility to spread around the world with considerable morbidity and mortality and presents an enormous burden on worldwide public health. Few mathematical models can be used because influenza incidence data are generally not normally distributed. We developed a mathematical model using Extreme Value Theory (EVT) to forecast the probability of outbreak of highly pathogenic influenza.MethodsThe incidence data of highly pathogenic influenza in Zhejiang province from April 2009 to November 2013 were retrieved from the website of Health and Family Planning Commission of Zhejiang Province. MATLAB “VIEM” toolbox was used to analyze data and modelling. In the present work, we used the Peak Over Threshold (POT) model, assuming the frequency as a Poisson process and the intensity to be Pareto distributed, to characterize the temporal variability of the long-term extreme incidence of highly pathogenic influenza in Zhejiang, China.ResultsThe skewness and kurtosis of the incidence of highly pathogenic influenza in Zhejiang between April 2009 and November 2013 were 4.49 and 21.12, which indicated a “fat tail” distribution. A QQ plot and a mean excess plot were used to further validate the features of the distribution. After determining the threshold, we modeled the extremes and estimated the shape parameter and scale parameter by the maximum likelihood method. The results showed that months in which the incidence of highly pathogenic influenza is about 4462/2286/1311/487 are predicted to occur once every five/three/two/one year, respectively.ConclusionsDespite the simplicity, the present study successfully offers the sound modeling strategy and a methodological avenue to implement forecasting of an epidemic in the midst of its course.     

Genetics,Receptor Binding Property,and Transmissibility in Mammals of Naturally Isolated H9N2 Avian Influenza Viruses

H9N2 subtype influenza viruses have been detected in different species of wild birds and domestic poultry in many countries for several decades. Because these viruses are of low pathogenicity in poultry, their eradication is not a priority for animal disease control in many countries, which has allowed them to continue to evolve and spread. Here, we characterized the genetic variation, receptor-binding specificity, replication capability, and transmission in mammals of a series of H9N2 influenza viruses that were detected in live poultry markets in southern China between 2009 and 2013. Thirty-five viruses represented 17 genotypes on the basis of genomic diversity, and one specific “internal-gene-combination” predominated among the H9N2 viruses. This gene combination was also present in the H7N9 and H10N8 viruses that have infected humans in China. All of the 35 viruses preferentially bound to the human-like receptor, although two also retained the ability to bind to the avian-like receptor. Six of nine viruses tested were transmissible in ferrets by respiratory droplet; two were highly transmissible. Some H9N2 viruses readily acquired the 627K or 701N mutation in their PB2 gene upon infection of ferrets, further enhancing their virulence and transmission in mammals. Our study indicates that the widespread dissemination of H9N2 viruses poses a threat to human health not only because of the potential of these viruses to cause an influenza pandemic, but also because they can function as “vehicles” to deliver different subtypes of influenza viruses from avian species to humans.     

The Influence of Angiotensin Converting Enzyme and Angiotensinogen Gene Polymorphisms on Hypertrophic Cardiomyopathy

Some studies have reported that angiotensin converting enzyme (ACE) and angiotensinogen (AGT) genes have been associated with hypertrophic cardiomyopathy (HCM). However, there have been inconsonant results among different studies. To clarify the influence of ACE and AGT on HCM, a systemic review and meta-analysis of case-control studies were performed. The following databases were searched to indentify related studies: PubMed database, the Embase database, the Cochrane Central Register of Controlled Trials database, China National Knowledge Information database, and Chinese Scientific and Technological Journal database. Search terms included “hypertrophic cardiomyopathy”, “angiotensin converting enzyme” (ACE) or “ACE” and “polymorphism or mutation”. For the association of AGT M235T polymorphism and HCM, “angiotensin converting enzyme” or “ACE” was replaced with “angiotensinogen”. A total of seventeen studies were included in our review. For the association of ACE I/D polymorphism and HCM, eleven literatures were included in the meta-analysis on association of penetrance and genotype. Similarly, six case-control studies were included in the meta-analysis for AGT M235T. For ACE I/D polymorphism, the comparison of DI/II genotype vs DD genotype was performed in the present meta-analysis. The OR was 0.73 (95% CI: 0.527, 0.998, P = 0.049, power = 94%, alpha = 0.05) after the study which deviated from Hardy-Weinberg Equilibrium was excluded, indicating that the ACE I/D gene polymorphism might be associated with HCM. The AGT M235T polymorphism did not significantly affect the risk of HCM. In addition, ACE I/D gene polymorphism did not significantly influence the interventricular septal thickness in HCM patients. In conclusion, the ACE I/D polymorphism might be associated with the risk of HCM.     

Common Sequence at the 5′ Ends of the Segmented RNA Genomes of Influenza A and B Viruses

Guanylyl- and methyltransferases, isolated from purified vaccinia virus, were used to specifically label the 5′ ends of the genome RNAs of influenza A and B viruses. All eight segments were labeled with [α-³²P]guanosine 5′-triphosphate or S-adenosyl[methyl-³H]methionine to form “cap” structures of the type m⁷G(5′)pppN^m-, of which unmethylated (p)ppN- represents the original 5′ end. Further analyses indicated that m⁷G(5′)pppA^m, m⁷G(5′)pppA^mpGp, and m⁷G(5′)pppA^mpGpUp were released from total and individual labeled RNA segments by digestion with nuclease P1, RNase T1, and RNase A, respectively. Consequently, the 5′-terminal sequences of most or all individual genome RNAs of influenza A and B viruses were deduced to be (p)ppApGpUp. The presence of identical sequences at the ends of RNA segments of both types of influenza viruses indicates that they have been specifically conserved during evolution.     

Unseasonal Transmission of H3N2 Influenza A Virus During the Swine-Origin H1N1 Pandemic

The initial wave of swine-origin influenza A virus (pandemic H1N1/09) in the United States during the spring and summer of 2009 also resulted in an increased vigilance and sampling of seasonal influenza viruses (H1N1 and H3N2), even though they are normally characterized by very low incidence outside of the winter months. To explore the nature of virus evolution during this influenza “off-season,” we conducted a phylogenetic analysis of H1N1 and H3N2 sequences sampled during April to June 2009 in New York State. Our analysis revealed that multiple lineages of both viruses were introduced and cocirculated during this time, as is typical of influenza virus during the winter. Strikingly, however, we also found strong evidence for the presence of a large transmission chain of H3N2 viruses centered on the south-east of New York State and which continued until at least 1 June 2009. These results suggest that the unseasonal transmission of influenza A viruses may be more widespread than is usually supposed.The recent emergence of swine-origin H1N1 influenza A virus (pandemic H1N1/09) in humans has heightened awareness of how the burden of morbidity and mortality due to influenza is associated with the appearance of new genetic variants (5) and of the genetic and epidemiological determinants of viral transmission (8). The emergence of pandemic H1N1/09 is also unprecedented in recorded history as it means that three antigenically distinct lineages of influenza A virus—pandemic H1N1/09 and the seasonal H1N1 and H3N2 viruses— currently cocirculate within human populations.Although the presence of multiple subtypes of influenza A virus may place an additional burden on public health resources, it also provides a unique opportunity to compare the patterns and dynamics of evolution in these viruses on a similar time scale. Indeed, one of the most interesting secondary effects of the current H1N1/09 pandemic has been an increased vigilance for cases of influenza-like illness and hence an intensified sampling of seasonal H1N1 and H3N2 viruses during the typical influenza “off-season” (i.e., spring-summer) in the northern hemisphere. Because the influenza season in the northern hemisphere generally runs from November through March, with a usual peak in January or February, influenza viruses sampled outside of this period are of special interest.The current model for the global spatiotemporal dynamics of influenza A virus is that the northern and southern hemispheres represent ecological “sinks” for this virus, with little ongoing viral transmission during the summer months (9). In contrast, more continual viral transmission occurs within the tropical “source” population (13) that is most likely centered on an intense transmission network in east and southeast Asia (10). However, the precise epidemiological and evolutionary reasons for this major geographic division, and for the seasonality of influenza A virus in general, remain uncertain (1, 4). Evidence for this “sink-source” ecological model is that viruses sampled from successive seasons in localities such as New York State do not usually form linked clusters on phylogenetic trees, indicating that they are not connected by direct transmission through the summer months (7). Similar conclusions can be drawn for the United States as a whole and point to multiple introductions of phylogenetically distinct lineages during the winter (6), followed by complex patterns of spatial diffusion (14). However, despite the growing epidemiological and phylogenetic data supporting this model, it is also evident that there is relatively little sequence data from seasonal influenza viruses that are sampled from April to October in the northern hemisphere. Hence, it is uncertain whether extended chains of transmission can occur during this time period, even though this may have an important bearing on our understanding of influenza seasonality.To address these issues, we examined the evolutionary behavior of seasonal H1N1 and H3N2 viruses as they cocirculated during a single time period—(late) April to June 2009—within a single locality (New York State). Not only are levels of influenza virus transmission in the northern hemisphere usually very low during this time period, but in this particular season the human host population was also experiencing the emerging epidemic of pandemic H1N1/09.     

Diverse Phage-Encoded Toxins in a Protective Insect Endosymbiont

The lysogenic bacteriophage APSE infects “Candidatus Hamiltonella defensa,” a facultative endosymbiont of aphids and other sap-feeding insects. This endosymbiont has established a beneficial association with aphids, increasing survivorship following attack by parasitoid wasps. Although APSE and “Ca. Hamiltonella defensa” are effectively maternally transmitted between aphid generations, they can also be horizontally transferred among insect hosts, which results in genetically distinct “Ca. Hamiltonella defensa” strains infecting the same aphid species and sporadic distributions of both APSE and “Ca. Hamiltonella defensa” among hosts. Aphids infected only with “Ca. Hamiltonella defensa” have significantly less protection than those infected with both “Ca. Hamiltonella defensa” and APSE. This protection has been proposed to be connected to eukaryote-targeted toxins previously discovered in the genomes of two characterized APSE strains. In this study, we have sequenced partial genomes from seven additional APSE strains to address the evolution and extent of toxin variation in this phage. The APSE lysis region has been a hot spot for nonhomologous recombination of novel virulence cassettes. We identified four new toxins from three protein families, Shiga-like toxin, cytolethal distending toxin, and YD-repeat toxins. These recombination events have also resulted in reassortment of the downstream lysozyme and holin genes. Analysis of the conserved APSE genes flanking the variable toxin cassettes reveals a close phylogenetic association with phage sequences from two other facultative endosymbionts of insects. Thus, phage may act as a conduit for ongoing gene exchange among heritable endosymbionts.     

Cooperativity Between CD8+ T Cells,Non-Neutralizing Antibodies,and Alveolar Macrophages Is Important for Heterosubtypic Influenza Virus Immunity

Seasonal epidemics of influenza virus result in ∼36,000 deaths annually in the United States. Current vaccines against influenza virus elicit an antibody response specific for the envelope glycoproteins. However, high mutation rates result in the emergence of new viral serotypes, which elude neutralization by preexisting antibodies. T lymphocytes have been reported to be capable of mediating heterosubtypic protection through recognition of internal, more conserved, influenza virus proteins. Here, we demonstrate using a recombinant influenza virus expressing the LCMV GP33-41 epitope that influenza virus-specific CD8+ T cells and virus-specific non-neutralizing antibodies each are relatively ineffective at conferring heterosubtypic protective immunity alone. However, when combined virus-specific CD8 T cells and non-neutralizing antibodies cooperatively elicit robust protective immunity. This synergistic improvement in protective immunity is dependent, at least in part, on alveolar macrophages and/or other lung phagocytes. Overall, our studies suggest that an influenza vaccine capable of eliciting both CD8+ T cells and antibodies specific for highly conserved influenza proteins may be able to provide heterosubtypic protection in humans, and act as the basis for a potential “universal” vaccine.     

Common SNPs in FTO Gene Are Associated with Obesity Related Anthropometric Traits in an Island Population from the Eastern Adriatic Coast of Croatia

Background

Multiple studies have provided compelling evidence that the FTO gene variants are associated with obesity measures. The objective of the study was to investigate whether FTO variants are associated with a broad range of obesity related anthropometric traits in an island population.

Methodology/Principal Findings

We examined genetic association between 29 FTO SNPs and a comprehensive set of anthropometric traits in 843 unrelated individuals from an island population in the eastern Adriatic coast of Croatia. The traits include 11 anthropometrics (height, weight, waist circumference, hip circumference, bicondilar upper arm width, upper arm circumference, and biceps, triceps, subscapular, suprailiac and abdominal skin-fold thicknesses) and two derived measures (BMI and WHR). Using single locus score tests, 15 common SNPs were found to be significantly associated with “body fatness” measures such as weight, BMI, hip and waist circumferences with P-values ranging from 0.0004 to 0.01. Similar but less significant associations were also observed between these markers and bicondilar upper arm width and upper arm circumference. Most of these significant findings could be explained by a mediating effect of “body fatness”. However, one unique association signal between upper arm width and rs16952517 (P-value = 0.00156) could not be explained by this mediating effect. In addition, using a principle component analysis and conditional association tests adjusted for “body fatness”, two novel association signals were identified between upper arm circumference and rs11075986 (P-value = 0.00211) and rs16945088 (P-value = 0.00203).

Conclusions/Significance

The current study confirmed the association of common variants of FTO gene with “body fatness” measures in an isolated island population. We also observed evidence of pleiotropic effects of FTO gene on fat-free mass, such as frame size and muscle mass assessed by bicondilar upper arm width and upper arm circumference respectively and these pleiotropic effects might be influenced by variants that are different from the ones associated with “body fatness”.