A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses.

Surface antigens of pathogens are commonly targeted by vaccine-elicited antibodies but antigenic variability, notably in RNA viruses such as influenza, HIV and SARS-CoV-2, pose challenges for control by vaccination. For example, influenza A(H3N2) entered the human population in 1968 causing a pandemic and has since been monitored, along with other seasonal influenza viruses, for the emergence of antigenic drift variants through intensive global surveillance and laboratory characterisation. Statistical models of the relationship between genetic differences among viruses and their antigenic similarity provide useful information to inform vaccine development, though accurate identification of causative mutations is complicated by highly correlated genetic signals that arise due to the evolutionary process. Here, using a sparse hierarchical Bayesian analogue of an experimentally validated model for integrating genetic and antigenic data, we identify the genetic changes in influenza A(H3N2) virus that underpin antigenic drift. We show that incorporating protein structural data into variable selection helps resolve ambiguities arising due to correlated signals, with the proportion of variables representing haemagglutinin positions decisively included, or excluded, increased from 59.8% to 72.4%. The accuracy of variable selection judged by proximity to experimentally determined antigenic sites was improved simultaneously. Structure-guided variable selection thus improves confidence in the identification of genetic explanations of antigenic variation and we also show that prioritising the identification of causative mutations is not detrimental to the predictive capability of the analysis. Indeed, incorporating structural information into variable selection resulted in a model that could more accurately predict antigenic assay titres for phenotypically-uncharacterised virus from genetic sequence. Combined, these analyses have the potential to inform choices of reference viruses, the targeting of laboratory assays, and predictions of the evolutionary success of different genotypes, and can therefore be used to inform vaccine selection processes.

Chlorhexidine versus saline in reducing the risk of catheter associated urinary tract infection: A cost-effectiveness analysis.

BACKGROUND: Catheter associated urinary tract infections are one of the most common infections acquired in hospital. A recent randomised control study demonstrated the benefit of using chlorhexidine (0.1%) for meatal cleaning prior to urinary catheter insertion, by reducing both catheter associated asymptomatic bacteriuria and infection. These findings raise the important question of whether a decision to switch from saline to chlorhexidine was likely to be cost-effective. The aim of this paper was to evaluate the cost-effectiveness of adopting routine use of chlorhexidine for meatal cleaning prior to urinary catheter insertion METHODS: The outcomes of this cost-effectiveness study are changes to health service costs in $AUD and changes to quality adjusted life years from a decision to adopt 0.1% chlorhexidine for meatal cleaning prior to urinary catheter insertion as compared to saline. Effectiveness outcomes for this study were taken from a 32 week stepped wedge randomised controlled study conducted in three Australian hospitals. RESULTS: The changes in health costs from switching from saline to 0.1% chlorhexidine per 100,000 catheterisations would save hospitals AUD$387,909 per 100,000 catherisations, prevent 70 cases of catheter associated urinary tract infections, release 282 bed days and provide a small improvement in health benefits of 1.43 quality adjusted life years. Using a maximum willingness to pay for a marginal quality adjusted life year threshold of AUD$28,000 per 100,000 catherisations, suggests that adopting chlorhexidine would be cost effective and potentially cost-saving. CONCLUSION: The findings from our work provide evidence to health system administrators and those responsible for drafting catheter associated urinary tract infections prevention guidelines that investing in switching from saline to chlorhexidine is not only clinically effective but also a sensible decision in the context of allocating finite healthcare resources.

Chlorhexidine for meatal cleaning in reducing catheter-associated urinary tract infections: a multicentre stepped-wedge randomised controlled trial.

BACKGROUND: Evidence for the benefits of antiseptic meatal cleaning in reducing catheter-associated urinary tract infection (UTI) is inconclusive. We assessed the efficacy of 0·1% chlorhexidine solution compared with normal saline for meatal cleaning before urinary catheter insertion in reducing the incidence of catheter-associated asymptomatic bacteriuria and UTI. METHODS: A cross-sectional, stepped-wedge, open-label, randomised controlled trial was undertaken in Australian hospitals. Eligible hospitals were Australian public and private hospitals, with an intensive care unit and more than 30 000 hospital admissions per year. Hospitals were randomly assigned to an intervention crossover date using a computer-generated randomisation system. Crossover dates occurred every 8 weeks; during the first 8 weeks of the study, no hospitals were exposed to the intervention (control phase), after which each hospital sequentially crossed over from the control to the intervention every 8 weeks. Patients requiring a urinary cathetwer were potentially eligible for inclusion in this hospital-wide study. Participants were excluded if they were younger than 2 years, had a medical reason preventing the use of the chlorhexidine, had the catheter inserted in theatre, did not have the catheter insertion date documented, required in-and-out or suprapubic catheterisation, had symptoms and signs suggestive of UTI at the time of catheter insertion, or were currently undergoing treatment for UTI. The intervention was the use of 0·1% chlorhexidine solution for meatal cleaning before urinary catheterisation with 0·9% normal saline used in the control phase. Masking of hospitals was not possible because it was not feasible to mask staff administering the intervention. The co-primary outcomes were the number of cases of catheter-associated asymptomatic bacteriuria and UTI per 100 catheter-days and were assessed within 7 days of catheter insertion in the intention-to-treat population. This trial is registered with Australian New Zealand Clinical Trials Registry, number ACTRN12617000373370. FINDINGS: 21 hospitals were assessed for eligibility between Jan 5, 2017, and May 1, 2017; of these, three were successfully enrolled and randomised to one of three intervention crossover dates. 1642 participants in these hospitals were included in the study between Aug 1, 2017, and March 12, 2018, 697 (42%) in the control phase and 945 (58%) in the intervention period. In the control period, 13 catheter-associated UTI and 29 catheter-associated asymptomatic bacteriuria events in 2889 catheter-days (0·45 catheter-associated UTI cases and 1·00 catheter-associated asymptomatic bacteriuria cases per 100 catheter-days) were recorded compared with four catheter-associated UTI and 16 catheter-associated asymptomatic bacteriuria events in 2338 catheter-days (0·17 catheter-associated UTI cases and 0·68 catheter-associated asymptomatic bacteriuria cases per 100 catheter-days) during the intervention period. The intervention was associated with a 74% reduction in the incidence of catheter-associated asymptomatic bacteriuria (incident rate ratio 0·26, 95% CI 0·08-0·86, p=0·026), and a 94% decrease in the incidence of catheter-associated UTI (0·06, 95% CI 0·01-0·32, p=0·00080). There were no reported adverse events. INTERPRETATION: The use of chlorhexidine solution for meatal cleaning before catheter insertion decreased the incidence of catheter-associated asymptomatic bacteriuria and UTI and has the potential to improve patient safety. FUNDING: HCF Research Foundation.

Reducing catheter-associated urinary tract infections in hospitals: study protocol for a multi-site randomised controlled study.

INTRODUCTION: Despite advances in infection prevention and control, catheter-associated urinary tract infections (CAUTIs) are common and remain problematic. A number of measures can be taken to reduce the risk of CAUTI in hospitals. Appropriate urinary catheter insertion procedures are one such method. Reducing bacterial colonisation around the meatal or urethral area has the potential to reduce CAUTI risk. However, evidence about the best antiseptic solutions for meatal cleaning is mixed, resulting in conflicting recommendations in guidelines internationally. This paper presents the protocol for a study to evaluate the effectiveness (objective 1) and cost-effectiveness (objective 2) of using chlorhexidine in meatal cleaning prior to catheter insertion, in reducing catheter-associated asymptomatic bacteriuria and CAUTI. METHODS AND ANALYSIS: A stepped wedge randomised controlled trial will be undertaken in three large Australian hospitals over a 32-week period. The intervention in this study is the use of chlorhexidine (0.1%) solution for meatal cleaning prior to catheter insertion. During the first 8 weeks of the study, no hospital will receive the intervention. After 8 weeks, one hospital will cross over to the intervention with the other two participating hospitals crossing over to the intervention at 8-week intervals respectively based on randomisation. All sites complete the trial at the same time in 2018. The primary outcomes for objective 1 (effectiveness) are the number of cases of CAUTI and catheter-associated asymptomatic bacteriuria per 100 catheter days will be analysed separately using Poisson regression. The primary outcome for objective 2 (cost-effectiveness) is the changes in costs relative to health benefits (incremental cost-effectiveness ratio) from adoption of the intervention. DISSEMINATION: Results will be disseminated via peer-reviewed journals and presentations at relevant conferences.A dissemination plan it being developed. Results will be published in the peer review literature, presented at relevant conferences and communicated via professional networks. ETHICS: Ethics approval has been obtained. TRIAL REGISTRATION NUMBER: 12617000373370, approved 13/03/2017. Protocol version 1.1.

Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses.

Determining phenotype from genetic data is a fundamental challenge. Identification of emerging antigenic variants among circulating influenza viruses is critical to the vaccine virus selection process, with vaccine effectiveness maximized when constituents are antigenically similar to circulating viruses. Hemagglutination inhibition (HI) assay data are commonly used to assess influenza antigenicity. Here, sequence and 3-D structural information of hemagglutinin (HA) glycoproteins were analyzed together with corresponding HI assay data for former seasonal influenza A(H1N1) virus isolates (1997-2009) and reference viruses. The models developed identify and quantify the impact of eighteen amino acid substitutions on the antigenicity of HA, two of which were responsible for major transitions in antigenic phenotype. We used reverse genetics to demonstrate the causal effect on antigenicity for a subset of these substitutions. Information on the impact of substitutions allowed us to predict antigenic phenotypes of emerging viruses directly from HA gene sequence data and accuracy was doubled by including all substitutions causing antigenic changes over a model incorporating only the substitutions with the largest impact. The ability to quantify the phenotypic impact of specific amino acid substitutions should help refine emerging techniques that predict the evolution of virus populations from one year to the next, leading to stronger theoretical foundations for selection of candidate vaccine viruses. These techniques have great potential to be extended to other antigenically variable pathogens.

Optimisation of a micro-neutralisation assay and its application in antigenic characterisation of influenza viruses.

OBJECTIVES: The identification of antigenic variants and the selection of influenza viruses for vaccine production are based largely on antigenic characterisation of the haemagglutinin (HA) of circulating viruses using the haemagglutination inhibition (HI) assay. However, in addition to evolution related to escape from host immunity, variants emerging as a result of propagation in different cell substrates can complicate the interpretation of HI results. The objective was to develop further a micro-neutralisation (MN) assay to complement the HI assay in antigenic characterisation of influenza viruses to assess the emergence of new antigenic variants and reinforce the selection of vaccine viruses. DESIGN AND SETTING: A 96-well-plate plaque reduction MN assay based on the measurement of infected cell population using a simple imaging technique. SAMPLE: Representative influenza A (H1N1) pdm09, A(H3N2) and B viruses isolated between 2004 and 2013 MAIN OUTCOME MEASURES AND RESULTS: Improvements to the plaque reduction MN assay included selection of the most suitable cell line according to virus type or subtype, and optimisation of experimental design and data quantitation. Comparisons of the results of MN and HI assays showed the importance of complementary data in determining the true antigenic relationships among recent human influenza A(H1N1)pdm09, A(H3N2) and type B viruses. CONCLUSIONS: Our study demonstrates that the improved MN assay has certain advantages over the HI assay: it is not significantly influenced by the cell-selected amino acid substitutions in the neuraminidase (NA) of A(H3N2) viruses, and it is particularly useful for antigenic characterisation of viruses which either grow to low HA titre and/or undergo an abortive infection resulting in an inability to form plaques in cultured cells.

Integrating influenza antigenic dynamics with molecular evolution.

Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001.

Sentinel surveillance for influenza in Senegal, 1996-2009.

BACKGROUND: Data on influenza in tropical and resource-limited countries are scarce. In this study we present results from 14 years of influenza surveillance in Senegal, one of the few tropical countries in Africa from which longitudinal data are available. METHODS: From 1996 to 2009, we collected respiratory specimens from outpatients presenting with influenza-like illness at 13 facilities in order to investigate the epidemiology of seasonal influenza and the characteristics of the circulating influenza viruses. Specimens were tested for influenza using viral isolation and/or reverse-transcription polymerase chain reaction (RT-PCR). RESULTS: From 1996 to 2009, specimens were obtained from 9176 patients; 1233 (13%) were influenza-positive by virus isolation and/or RT-PCR. Among positive samples, 958 (77%) were influenza A, 268 (22%) influenza B, and 7 (1%) influenza type C; of influenza A viruses, 619 (65%) were A(H3) and 339 (35%) A(H1), of which 13 (1%) were identified as H1N2. The proportion positive was similar for children <15 years, young adults 16-35 years, and adults 36-55 years (15%), but lower for persons >55 years (9%). Although influenza A(H1), A(H3), and B all circulated during most years, influenza A(H3N2) predominated during 9 of the 14 years. Influenza activity consistently peaked during the rainy season (July-September). Phylogenetic analysis showed that viruses circulating in Senegal were similar to contemporary viruses circulating elsewhere in the world. CONCLUSIONS: Our data confirm that influenza is prevalent in Senegal, occurs in seasonal epidemics, and contributes to the burden of respiratory diseases in all age groups.

Amantadine resistance in relation to the evolution of influenza A(H3N2) viruses in Iran.

The aminoadamantanes, amantadine and rimantadine, have been used to prevent and treat influenza A virus infections for many years. Several reports have shown an increased level of resistance to these drugs, particularly among influenza A(H3N2) subtype viruses, during recent years. We observed an increase in amantadine resistance, due to a Ser31Asn mutation in the M2 channel protein, among A(H3N2) viruses circulating in Iran during 2005-2007. Sequence analyses of the haemagglutinin and neuraminidase genes as well as the M gene of these viruses revealed that the emergence of resistance was in general consistent with the progressive worldwide evolution of H3N2 viruses.

Altered receptor specificity and cell tropism of D222G hemagglutinin mutants isolated from fatal cases of pandemic A(H1N1) 2009 influenza virus.

Mutations in the receptor-binding site of the hemagglutinin of pandemic influenza A(H1N1) 2009 viruses have been detected sporadically. An Asp222Gly (D222G) substitution has been associated with severe or fatal disease. Here we show that 222G variants infected a higher proportion of ciliated cells in cultures of human airway epithelium than did viruses with 222D or 222E, which targeted mainly nonciliated cells. Carbohydrate microarray analyses showed that 222G variants bind a broader range of α2-3-linked sialyl receptor sequences of a type expressed on ciliated bronchial epithelial cells and on epithelia within the lung. These features of 222G mutants may contribute to exacerbation of disease.

Neuraminidase receptor binding variants of human influenza A(H3N2) viruses resulting from substitution of aspartic acid 151 in the catalytic site: a role in virus attachment?

Changes in the receptor binding characteristics of human H3N2 viruses have been evident from changes in the agglutination of different red blood cells (RBCs) and the reduced growth capacity of recently isolated viruses, particularly in embryonated eggs. An additional peculiarity of viruses circulating in 2005 to 2009 has been the poor inhibition of hemagglutination by postinfection ferret antisera for many viruses isolated in MDCK cells, including homologous reference viruses. This was shown not to be due to an antigenic change in hemagglutinin (HA) but was shown to be the result of a mutation in aspartic acid 151 of neuraminidase (NA) to glycine, asparagine, or alanine, which caused an oseltamivir-sensitive agglutination of RBCs. The D151G substitution was shown to cause a change in the specificity of NA such that it acquired the capacity to bind receptors, which were refractory to enzymatic cleavage, without altering its ability to remove receptors for HA. Thus, the inhibition of NA-dependent agglutination by the inclusion of oseltamivir carboxylate in the assay was effective in restoring the anti-HA specificity of the hemagglutination inhibition (HI) assay for monitoring antigenic changes in HA. Since the NA-dependent binding activity did not affect virus neutralization, and virus populations in clinical specimens possessed, at most, low levels of the "151 mutant," the biological significance of this feature of NA in, for example, immune evasion is unclear. It is apparent, however, that an important role of aspartic acid 151 in the activity of NA may be to restrict the specificity of the NA interaction and its receptor-destroying activity to complement that of HA receptor binding.

Circulation of human influenza viruses and emergence of Oseltamivir-resistant A(H1N1) viruses in Cameroon, Central Africa.

BACKGROUND: While influenza surveillance has increased in most developing countries in the last few years, little influenza surveillance has been carried out in sub-Saharan Africa and no information is available in Central Africa. The objective of this study was to assess the prevalence of influenza viruses circulating in Yaounde, Cameroon and determine their antigenic and genetic characteristics. METHODS: Throat and/or nasal swabs were collected from November 2007 to October 2008 from outpatients with influenza-like illness (ILI) in Yaounde, Cameroon and analyzed by two different techniques: a one-step real time reverse transcription-polymerase chain reaction (RT-PCR) and virus isolation in MDCK cells. Typing and subtyping of virus isolates was performed by hemagglutination inhibition (HI), and viruses were sent to the WHO Collaborating Centre in London, UK for further characterization and analyses of antiviral resistance by enzyme inhibition assay and nucleotide sequencing. RESULTS: A total of 238 patients with ILI were sampled. During this period 70 (29%) samples were positive for influenza by RT-PCR, of which only 26 (11%) were positive by virus isolation. By HI assay, 20 of the 26 isolates were influenza type A (10 H3N2 and 10 H1N1) and 6 were influenza type B (2 B/Victoria/2/87 lineage and 4 B/Yagamata/16/88 lineage). Seven (70%) of the H1N1 isolates were shown to be resistant to oseltamivir due to a H275Y mutation. CONCLUSIONS: This study confirmed the circulation of influenza A(H1N1), A(H3N2) and B viruses in the human population in Central Africa and describes the emergence of oseltamivir-resistant A(H1N1) viruses in Central Africa.

Influenza virus infection in travelers to tropical and subtropical countries.

BACKGROUND: Influenza outbreaks have been reported among travelers, but attack rates and incidence are unknown. METHODS: A cohort study was conducted. Travelers to subtropical and tropical countries recruited at the University of Zurich Travel Clinic (Switzerland), January 1998 to March 2000, were investigated with pre- and posttravel assessment of hemagglutination inhibition and by questionnaire. RESULTS: Among 1450 travelers recruited who completed questionnaires and provided serum samples before departure, 289 (19.9%) reported febrile illness during or after traveling abroad; of these, 211 (73.0%) provided paired serum samples. Additionally, paired serum samples were collected from 321 frequency-matched afebrile control subjects among the remaining 1161 subjects of the study population. Seroconversion for influenza virus infection was demonstrated in 40 (2.8%) of all travelers; 18 participants (1.2%) had a > or = 4-fold increase in antibody titers. This corresponds to an incidence of 1.0 influenza-associated events per 100 person-months abroad. Among the 211 febrile participants, 27 (12.8%) had seroconversion, 13 (6.2%) with a > or = 4-fold increase; among the 321 afebrile control subjects, 13 (4.0%) had seroconversion, 5 (1.6%) with a > or = 4-fold increase. Twenty-five seroconverters (62.5%; P = .747) acquired influenza outside of the European epidemic season. Sixteen patients (40.0%) sought medical attention either abroad or at home, and 32 (80.0%) were asymptomatic at the time of completion of the survey. CONCLUSIONS: This survey indicates that influenza is the most frequent vaccine-preventable infection among travelers to subtropical and tropical countries. Infections occur mainly outside the domestic epidemic season, and they have a considerable impact. Pretravel vaccination should be considered for travelers to subtropical and tropical countries.

Changes in the hemagglutinins and neuraminidases of human influenza B viruses isolated in Italy during the 2001-02, 2002-03, and 2003-04 seasons.

Throughout most of the last decade, B/Yamagata/16/88-lineage influenza viruses were predominant among the B isolates circulating worldwide, whereas B/Victoria/2/87-lineage viruses were isolated infrequently and restricted geographically to eastern Asia. During the 2001-02 influenza season, B/Victoria/2/87-lineage viruses re-emerged in North America and Europe and spread worldwide. Virological surveillance in Italy during that season showed wide circulation of influenza B viruses, of which most were antigenically related to the B/Sichuan/379/99 (Yamagata-lineage) vaccine strain, together with a smaller number of B viruses antigenically similar to B/HongKong/330/01, a recent B/Victoria/2/87-lineage antigenic variant. In the subsequent 2002-03 epidemic season, B viruses with a Victoria-lineage hemagglutinin (HA), more closely related to that of B/Shandong/7/97, were isolated exclusively. Similar strains have continued to predominate among the few B viruses isolated in Italy during last season (2003-04), although most influenza B viruses, isolated sporadically elsewhere in Europe, again belong to the Yamagata-lineage. In the present study, phylogenetic analyses of the HA and neuraminidase (NA) genes of representative B strains, isolated throughout Italy during 2001-04, showed that during the first influenza season the NA genes, as well as the HA genes, separated into the two distinct clades, the Yamagata- and Victoria-lineages, and showed no evidence of genetic reassortment. On the contrary, all the B viruses isolated in the 2002-03 and most of those isolated in the 2003-04 epidemic season were "Victoria HA-Yamagata NA" reassortants similar to those isolated in other parts of the world, showing that these reassortants became established in the human population. The frequency of reassortment between HA and NA of distinct lineages and sublineages highlights again the importance of detailed molecular analyses of both surface glycoproteins in understanding the evolution of influenza B viruses.

A summer outbreak of influenza A virus infection among young children.

In the summer of 2003 in Jerusalem, Israel, 23 children were hospitalized with influenza A virus (A/Fujian/411/02-like virus) infection. The majority were neonates and infants. Clinical manifestations included neonatal fever, bronchitis, bronchiolitis, and pneumonia, and outcomes were favorable. Continued surveillance between epidemic seasons could allow early recognition of influenza strains that will appear in the following influenza season.

Molecular characterization of influenza B viruses circulating in northern Italy during the 2001-2002 epidemic season.

During the 2001-2002 influenza season, virological surveillance highlighted the predominant circulation of B viruses (86% of isolates) in Italy, in contrast to many other countries in Europe and North America where AH3N2 viruses were isolated most frequently, and in contrast to the infrequent isolation of B viruses in Italy during the previous two years. Associated with this predominance of influenza B was the re-emergence of B/Victoria/2/87-lineage viruses, closely related to B viruses prevalent during the 1980s, which are distinct antigenically and genetically from circulating B/Sichuan/379/99-like viruses of the B/Yamagata/16/88 lineage, which predominated in most parts of the world during the last 10 years. Ninety-four viruses isolated in two regions of northern Italy were characterized, 50 by direct sequencing of haemagglutinin (HA). Viruses of both Victoria and Yamagata lineages co-circulated throughout the 12 weeks of the influenza season. The HAs of the Yamagata-lineage viruses were heterogeneous and comprised two sublineages, represented by B/Sichuan/379/99 and B/Harbin/7/94, whereas the Victoria-lineage viruses were more homogeneous and closely related to B/Hong Kong/330/01, the current prototype vaccine strain. The antigenic and genetic characteristics of the viruses correlated with certain epidemiological features. In particular, the low age (<14 years) of individuals infected with B/Hong Kong/330/01-like viruses is likely to reflect the greater susceptibility of the youngest cohort, due to lack of previous exposure to Victoria-lineage viruses, and is consistent with the conclusion that vaccination with a B/Sichuan/379/99-like virus would give poor protection against infection with B/Hong Kong/330/01-like (Victoria-lineage) viruses.