A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2.

There is great potential for host-based gene expression analysis to impact the early diagnosis of infectious diseases. In particular, the influenza pandemic of 2009 highlighted the challenges and limitations of traditional pathogen-based testing for suspected upper respiratory viral infection. We inoculated human volunteers with either influenza A (A/Brisbane/59/2007 (H1N1) or A/Wisconsin/67/2005 (H3N2)), and assayed the peripheral blood transcriptome every 8 hours for 7 days. Of 41 inoculated volunteers, 18 (44%) developed symptomatic infection. Using unbiased sparse latent factor regression analysis, we generated a gene signature (or factor) for symptomatic influenza capable of detecting 94% of infected cases. This gene signature is detectable as early as 29 hours post-exposure and achieves maximal accuracy on average 43 hours (p = 0.003, H1N1) and 38 hours (p-value = 0.005, H3N2) before peak clinical symptoms. In order to test the relevance of these findings in naturally acquired disease, a composite influenza A signature built from these challenge studies was applied to Emergency Department patients where it discriminates between swine-origin influenza A/H1N1 (2009) infected and non-infected individuals with 92% accuracy. The host genomic response to Influenza infection is robust and may provide the means for detection before typical clinical symptoms are apparent.

Temporal dynamics of host molecular responses differentiate symptomatic and asymptomatic influenza a infection.

Exposure to influenza viruses is necessary, but not sufficient, for healthy human hosts to develop symptomatic illness. The host response is an important determinant of disease progression. In order to delineate host molecular responses that differentiate symptomatic and asymptomatic Influenza A infection, we inoculated 17 healthy adults with live influenza (H3N2/Wisconsin) and examined changes in host peripheral blood gene expression at 16 timepoints over 132 hours. Here we present distinct transcriptional dynamics of host responses unique to asymptomatic and symptomatic infections. We show that symptomatic hosts invoke, simultaneously, multiple pattern recognition receptors-mediated antiviral and inflammatory responses that may relate to virus-induced oxidative stress. In contrast, asymptomatic subjects tightly regulate these responses and exhibit elevated expression of genes that function in antioxidant responses and cell-mediated responses. We reveal an ab initio molecular signature that strongly correlates to symptomatic clinical disease and biomarkers whose expression patterns best discriminate early from late phases of infection. Our results establish a temporal pattern of host molecular responses that differentiates symptomatic from asymptomatic infections and reveals an asymptomatic host-unique non-passive response signature, suggesting novel putative molecular targets for both prognostic assessment and ameliorative therapeutic intervention in seasonal and pandemic influenza.

Enhancing pnemonia surveillance in acute care facilities in post SARS era : a Canadian hospital surveillance study, 2003-2004 influenza season

A retrospective study of patients hospitalized with influenza and/or pneumonia in a Niagara area community hospital for the influenza season 2003-04 was designed with the main goal of enhancing pneumonia surveillance in acute care facilities and the following specific objectives: 1) identify etiologies, factors, and clinical presentation associated with pneumonia; 2) assess the ODIN score on ICU patients to predict outcomes of severe pneumonia; 3) identify the frequency of pneumonia and influenza in a hospital setting; and 4) develop a hospital pneumonia electronic surveillance tool. A total of 172 patients' charts (50% females) were reviewed and classified into two groups: those with diagnosis of pneumonia (n=132) and those without pneumonia (n=40). The latter group consisted mainly of patients with influenza (85%). Most patients were young (<10yrs) or elderly (>71yrs). Presenting body temperature <38°C, cough symptoms, respiratory and cardiac precomorbidities were common in both groups. Pneumonia was more frequent in males (p= .032) and more likely community-acquired (98%) than nosocomial (2%). No evidence of ventilator-associated pneumonia was found. Microbiology testing in 72% of cases detected 19 different pathogens. In pneumonia patients the most common organisms were Streptococcus pneumoniae (3%), Respiratory syncytial virus (4%), and Influenza A virus (2%). Conversely, Influenza A virus was identified in 73% of non-pneumonia patients. Community-acquired influenza was more common (80%) than nosocomial influenza (20%). The ODIN score was a good predictor of mortality and the new electronic surveillance tool was an effective prototype to monitor patients in acute care, especially during influenza season. The results of this study provided baseline data on respiratory illness surveillance and demonstrated that future research, including prospective studies, is warranted in acute care facilities.

NS1 proteins of avian influenza A viruses can act as antagonists of the human alpha/beta interferon response

Many viruses, including human influenza A virus, have developed strategies for counteracting the host type I interferon (IFN) response. We have explored whether avian influenza viruses were less capable of combating the type I IFN response in mammalian cells, as this might be a determinant of host range restriction. A panel of avian influenza viruses isolated between 1927 and 1997 was assembled. The selected viruses showed variation in their ability to activate the expression of a reporter gene under the control of the IFN-beta promoter and in the levels of IFN induced in mammalian cells. Surprisingly, the avian NS1 proteins expressed alone or in the genetic background of a human influenza virus controlled IFN-beta induction in a manner similar to the NS1 protein of human strains. There was no direct correlation between the IFN-beta induction and replication of avian influenza viruses in human A549 cells. Nevertheless, human cells deficient in the type I IFN system showed enhanced replication of the avian viruses studied, implying that the human type I IFN response limits avian influenza viruses and can contribute to host range restriction.

Variation in the ability of human influenza A viruses to induce and inhibit the IFN-beta pathway

We investigated the ability of a selection of human influenza A viruses, including recent clinical isolates, to induce IFN-beta production in cultured cell lines. In contrast to the well-characterized laboratory strain A/PR/8/34, several, but not all, recent isolates of H3N2 viruses resulted in moderate IFN-beta stimulation. Through the generation of recombinant viruses, we were able to show that this is not due to a loss of the ability of the NS1 genes to suppress IFN-beta induction; indeed, the NS1 genes behaved similarly with respect to their abilities to block dsRNA signaling. Interestingly, replication of A/Sydney/5/97 virus was less Susceptible to pre-treatment with IFN-alpha than the other viruses. In contrast to the universal effect on dsRNA signaling, we noted differences in the effect of NS1 proteins on expression of interferon stimulated genes and also genes induced by a distinct pathway. The majority of NS1 proteins blocked expression From both IFN-dependent and TNF-dependent promoters by an apparent post-transcriptional mechanism. The NS1 gene of A/PR/8/34 NS1 did not confer these blocks. We noted striking differences in the Cellular localization of different influenza A virus NS1 proteins during infection, which might explain differences in biological activity. (C) 2005 Elsevier Inc. All rights reserved.

Characterization of recombinant influenza B viruses with key neuraminidase inhibitor resistance mutations

Objectives and methods: An influenza B virus plasmid-based rescue system was used to introduce site-specific mutations, previously observed in neuraminidase (NA) inhibitor-resistant viruses, into the NA protein of six recombinant viruses. Three mutations observed only among in vitro selected zanamivir-resistant influenza A mutants were introduced into the B/Beijing/1/87 virus NA protein, to change residue E116 to glycine, alanine or aspartic acid. Residue E116 was also mutated to valine, a mutation found in the clinic among oseltamivir-resistant viruses. An arginine to lysine change at position 291 (292 N2 numbering) mimicked that seen frequently in influenza A N2 clinical isolates resistant to oseltamivir. Similarly, an arginine to lysine change at position 149 (152 in N2 numbering) was made to reproduce the change found in the only reported zanamivir-resistant clinical isolate of influenza B virus. In vitro selection and prolonged treatment in the clinic leads to resistance pathways that require compensatory mutations in the haemagglutinin gene, but these appear not to be important for mutants isolated from immunocompetent patients. The reverse genetics system was therefore used to generate mutants containing only the NA mutation. Results and conclusions: With the exception of a virus containing the E116G mutation, mutant viruses were attenuated to different levels in comparison with wild-type virus. This attenuation was a result of altered NA activity or stability depending on the introduced mutation. Mutant viruses displayed increased resistance to zanamivir, oseltamivir and peramivir, with certain viruses displaying cross-resistance to all three drugs.

How to find natural reservoir hosts from endemic prevalence in a multi-host population : a case study of influenza in waterfowl

The transmission dynamics of infectious diseases critically depend on reservoir hosts, which can sustain the pathogen (or maintain the transmission) in the population even in the absence of other hosts. Although a theoretical foundation of the transmission dynamics in a multi-host population has been established, no quantitative methods exist for the identification of natural reservoir hosts. For a host to maintain the transmission alone, the host-specific reproduction number (U), interpreted as the average number of secondary transmissions caused by a single primary case in the host(s) of interest in the absence of all other hosts, must be greater than unity. If the host-excluded reproduction number (Q), representing the average number of secondary transmissions per single primary case in other hosts in the absence of the host(s) of interest, is below unity, transmission cannot be maintained in the multi-host population in the absence of the focal host(s).

The present study proposes a simple method for the identification of reservoir host(s) from observed endemic prevalence data across a range of host species. As an example, we analyze an aggregated surveillance dataset of influenza A virus in wild birds among which dabbling ducks exhibit higher prevalence compared to other bird species. Since the heterogeneous contact patterns between different host species are not directly observable, we test four different contact structures to account for the uncertainty. Meeting the requirements of U > 1 and Q < 1 for all four different contact structures, mallards and other dabbling ducks most likely constitute the reservoir community which plays a predominant role in maintaining the transmission of influenza A virus in the water bird population. We further discuss epidemiological issues which are concerned with the interpretation of influenza prevalence data, identifying key features to be fully clarified in the future.

A gel-capture assay for characterizing the sialyl-glycan selectivity of influenza viruses

Sialic acids (SA) usually linked to galactose (Gal) in an α2,6- or α2,3-configuration are considered the main cell receptors for influenza viruses, in particular for their hemagglutinins (HA). The typing of influenza virus HA receptor selectivity is relevant for understanding the transmissibility of avian and swine viruses to the human population. In this study we developed a simple and inexpensive gel-capture assay (GCA) of the influenza virus HA receptor-binding selectivity. Its principle is the binding of soluble influenza virus to pentasaccharide analogs, representatives of receptors of human and avian influenza viruses, immobilized on a gel resin. The human and avian analogs consisted of a sialyllactose-N-tetraose c (LSTc) [Neu5Ac(α2,6)Gal(β1-3)GlcNAc(β1-3)Gal(β1-4)Glc] and a sialyllactose-N-tetraose a (LSTa) [Neu5Ac(α2,3)Gal(β1-3)GlcNAc(β1-3)Gal(β1-4)Glc], respectively. Following equilibration, the unbound virus is washed away and the bound one is assayed via HA by densitometry as a function of the analog concentration. Using GCA, the receptor selectivity of three influenza viruses of different HA subtype was investigated. The results showed that the egg-adapted A/California/07/2009 (H1N1) virus exhibited an avian α2,3-linked LSTa selectivity, however, it retained the ability to bind to the α2,6-linked LSTc human receptor analog. Influenza B virus B/Florida/4/2006 showed α2,6-linked LSTc selectivity and a poor α2,3-linked LSTa avidity. The H3N2 virus A/Wisconsin/15/2009 displayed almost comparable avidity for both receptor analogs with a marginally greater α2,3-linked LSTa avidity. The described assay protocol provides a simple and rapid method for the characterization of influenza virus HA receptor binding selectivity. Keywords: influenza virus; hemagglutinin; receptor; sialyllactose-N-tetraose; gel-capture assay.

Effects of infection-induced migration delays on the epidemiology of avian influenza in wild mallard populations

Wild waterfowl populations form a natural reservoir of Avian Influenza (AI) virus, and fears exist that these birds may contribute to an AI pandemic by spreading the virus along their migratory flyways. Observational studies suggest that individuals infected with AI virus may delay departure from migratory staging sites. Here, we explore the epidemiological dynamics of avian influenza virus in a migrating mallard (Anas platyrhynchos) population with a specific view to understanding the role of infection-induced migration delays on the spread of virus strains of differing transmissibility. We develop a host-pathogen model that combines the transmission dynamics of influenza with the migration, reproduction and mortality of the host bird species. Our modeling predicts that delayed migration of individuals influences both the timing and size of outbreaks of AI virus. We find that (1) delayed migration leads to a lower total number of cases of infection each year than in the absence of migration delay, (2) when the transmission rate of a strain is high, the outbreak starts at the staging sites at which birds arrive in the early part of the fall migration, (3) when the transmission rate is low, infection predominantly occurs later in the season, which is further delayed when there is a migration delay. As such, the rise of more virulent AI strains in waterfowl could lead to a higher prevalence of infection later in the year, which could change the exposure risk for farmed poultry. A sensitivity analysis shows the importance of generation time and loss of immunity for the effect of migration delays. Thus, we demonstrate, in contrast to many current transmission risk models solely using empirical information on bird movements to assess the potential for transmission, that a consideration of infection-induced delays is critical to understanding the dynamics of AI infection along the entire flyway.

The epidemiology of the first wave of H1N1 influenza pandemic in Australia : a population-based study

Objectives: Following the recent H1N1 influenza pandemic we were able to describe seropositivity in a repre-sentative sample of adults prior to the availability of a specific vaccine.

Methods: This cross-sectional serological study is set in the Barwon Statistical Division, Australia. Blood samples were collected from September 2009 through to May 2010, from 1184 individuals (569 men, 615 women; median age 61.7 years), randomly selected from electoral rolls. Serum was analysed for specific H1N1 immunity using a haemagglutina-tion inhibition test. A self-report provided information about symptoms, demographics and healthcare. Associations be-tween H1N1 infection, gender, households and occupation were determined using logistic regression, adjusting for age.

Results: Of 1184 individuals, 129 (58 men, 71 women) were seropositive. Gender-adjusted age-specific prevalence was: 8.3% 20-29 years, 13.5% 30-39, 10.4% 40-49, 6.5% 50-59, 9.7% 60-69, 10.3% 70-79, 18.8% 80+. Standardised preva-lence was 10.3% (95%CI 9.6-11.0). No associations were detected between seropositivity and gender (OR=0.82, 95%CI 0.57-1.19) or being a healthcare worker (OR=1.43, 95%CI 0.62-3.29). Smokers (OR=1.86, 95%CI 1.09-3.15) and those socioeconomically disadvantaged (OR=2.52, 95%CI 1.24-5.13) were at increased risk. Among 129 seropositive individu-als, 31 reported symptoms that were either mild (n = 13) or moderate (time off work, doctor visit, n = 18). For age <60, 39.6% of seropositive individuals reported symptoms, whereas the proportion was 13.2% for age 60+.

Conclusions: Following the pandemic, the proportion of seropositive adults was low, but significant subclinical infection was found. Social disadvantage increased the likelihood of infection. The low symptom rate for older ages may relate to pre-existing immunity.

The 2007 outbreak of equine influenza in Australia: lessons learned for international trade in horses

In August 2007 Australia experienced its first outbreak of equine influenza. The disease occurred first in a quarantine station for imported horses near Sydney and subsequently escaped into the general horse population. After an extensive campaign the disease was eradicated and Australia is again recognised as free of this disease. Equine influenza was then, and is now, recognised to be the major disease risk associated with live horse imports into Australia and measures designed to mitigate this risk formed the basis of the quarantine protocols then in place. Subsequent investigations into the cause of the outbreak identified failures in compliance with these quarantine requirements as a contributing factor. It is also likely that the immunity of horses vaccinated as part of the import protocol was less than optimal, and that this had a significant role to play in the escape of the disease from quarantine.

Inhibition of reactive oxygen species production ameliorates inflammation induced by influenza A viruses via upregulation of SOCS1 and SOCS3.

Highly pathogenic avian influenza virus infection is associated with severe mortality in both humans and poultry. The mechanisms of disease pathogenesis and immunity are poorly understood although recent evidence suggests that cytokine/chemokine dysregulation contributes to disease severity following H5N1 infection. Influenza A virus infection causes a rapid influx of inflammatory cells, resulting in increased reactive oxygen species production, cytokine expression, and acute lung injury. Proinflammatory stimuli are known to induce intracellular reactive oxygen species by activating NADPH oxidase activity. We therefore hypothesized that inhibition of this activity would restore host cytokine homeostasis following avian influenza virus infection. A panel of airway epithelial and immune cells from mammalian and avian species were infected with A/Puerto Rico/8/1934 H1N1 virus, low-pathogenicity avian influenza H5N3 virus (A/duck/Victoria/0305-2/2012), highly pathogenic avian influenza H5N1 virus (A/chicken/Vietnam/0008/2004), or low-pathogenicity avian influenza H7N9 virus (A/Anhui/1/2013). Quantitative real-time reverse transcriptase PCR showed that H5N1 and H7N9 viruses significantly stimulated cytokine (interleukin-6, beta interferon, CXCL10, and CCL5) production. Among the influenza-induced cytokines, CCL5 was identified as a potential marker for overactive immunity. Apocynin, a Nox2 inhibitor, inhibited influenza-induced cytokines and reactive oxygen species production, although viral replication was not significantly altered in vitro. Interestingly, apocynin treatment significantly increased influenza virus-induced mRNA and protein expression of SOCS1 and SOCS3, enhancing negative regulation of cytokine signaling. These findings suggest that apocynin or its derivatives (targeting host responses) could be used in combination with antiviral strategies (targeting viruses) as therapeutic agents to ameliorate disease severity in susceptible species.

Epitope-specific CD4+, but not CD8+, T-cell responses induced by recombinant influenza A viruses protect against Mycobacterium tuberculosis infection

Tuberculosis remains a global health problem, in part due to failure of the currently available vaccine, BCG, to protect adults against pulmonary forms of the disease. We explored the impact of pulmonary delivery of recombinant influenza A viruses (rIAVs) on the induction of Mycobacterium tuberculosis (M. tuberculosis)-specific CD4(+) and CD8(+) T-cell responses and the resultant protection against M. tuberculosis infection in C57BL/6 mice. Intranasal infection with rIAVs expressing a CD4(+) T-cell epitope from the Ag85B protein (PR8.p25) or CD8(+) T-cell epitope from the TB10.4 protein (PR8.TB10.4) generated strong T-cell responses to the M. tuberculosis-specific epitopes in the lung that persisted long after the rIAVs were cleared. Infection with PR8.p25 conferred protection against subsequent M. tuberculosis challenge in the lung, and this was associated with increased levels of poly-functional CD4(+) T cells at the time of challenge. By contrast, infection with PR8.TB10.4 did not induce protection despite the presence of IFN-γ-producing M. tuberculosis-specific CD8(+) T cells in the lung at the time of challenge and during infection. Therefore, the induction of pulmonary M. tuberculosis epitope-specific CD4(+), but not CD8(+) T cells, is essential for protection against acute M. tuberculosis infection in the lung.

Antibodies to Influenza and West Nile Viruses in Horses in Mexico

INFLUENZA A virus (IAV) (family Orthomyxoviridae) is a highly infectious respiratory pathogen of birds and mammals, including human beings and horses (Palese and Shaw 2007). The virus is classified into different subtypes based on the antigenic properties of the haemagglutinin (HA) and neuraminidase (NA) proteins. Sixteen HA subtypes (H1 to H16) and nine NA subtypes (N1 to N9) have been identified (Fouchier and others 2005). Two subtypes, H3N8 and H7N7, have been isolated from horses. The H7N7 subtype was first isolated from a horse in Czechoslovakia in 1956 (Prague/56) (Sovinova and others 1958), and the H3N8 subtype was first isolated from a horse in Miami, USA, in 1963 (Waddell and others 1963). The H7N7 subtype has not been isolated from horses for three decades and is presumed to be extinct (Webster 1993). The H3N8 subtype is currently a common cause of disease in horses worldwide. In horses, influenza is characterized by an abrupt onset of pyrexia, depression, coughing and nasal discharge, and is often complicated by secondary bacteria infections that can lead to pneumonia and death (Hannant and Mumford 1996). Although H3N8 is a major cause of morbidity in horses throughout the world, information on the seroprevalence of IAV in horses and other domestic animals in Mexico is limited.

Caratterizzazione genomica di virus influenzali suini in Italia mediante next generation sequencing

I sottotipi H1N1, H1N2 e H3N2 di influenza A virus sono largamente diffusi nella popolazione suina di tutto il mondo. Nel presente lavoro è stato sviluppato un protocollo di sequenziamento di c.d. nuova generazione, su piattaforma Ion Torrent PGM, idoneo per l’analisi di tutti i virus influenzali suini (SIV). Per valutare l’evoluzione molecolare dei SIV italiani, sono stati sequenziati ed analizzati mediante analisi genomica e filogenetica un totale di sessantadue ceppi di SIV appartenenti ai sottotipi H1N1, H1N2 e H3N2, isolati in Italia dal 1998 al 2014. Sono stati evidenziati in sei campioni due fenomeni di riassortimento: tutti i SIV H1N2 esaminati presentavano una neuraminidasi di derivazione umana, diversa da quella dei SIV H1N2 circolanti in Europa, inoltre l’emoagglutinina (HA) di due isolati H1N2 era originata dal riassortimento con un SIV H1N1 avian-like. L’analisi molecolare dell’HA ha permesso di rivelare un’inserzione di due amminoacidi in quattro SIV H1N1 pandemici e una delezione di due aminoacidi in quattro SIV H1N2, entrambe a livello del sito di legame con il recettore cellulare. E’ stata inoltre evidenziata un’elevata omologia di un SIV H1N1 con ceppi europei isolati negli anni ’80, suggerendo la possibile origine vaccinale di questo virus. E’ stato possibile, in aggiunta, applicare il nuovo protocollo sviluppato per sequenziare un virus influenzale aviare altamente patogeno trasmesso all’uomo, direttamente da campione biologico. La diversità genetica nei SIV esaminati in questo studio conferma l’importanza di un continuo monitoraggio della costellazione genomica dei virus influenzali nella popolazione suina.