Mapping of the US Domestic Influenza Virologic Surveillance Landscape

Surveillance of the respiratory syncytial virus outside infancy: impact of testing methods, a retrospective observational study

Background

The European Medicines Agency has approved several vaccines to protect the elderly against respiratory syncytial virus (RSV) infections. However, differences in performance between antigen and PCR tests, especially in adults, can make monitoring RSV difficult. This study aims to assess the impact of the chosen diagnostic methods on the surveillance of RSV.

Methods

RSV and influenza test results obtained from July 2022 to June 2023 in a consolidated clinical laboratory in Brussels, Belgium, were collected. These results included antigen tests, quadruplex PCR tests and viral cultures on respiratory samples. Epidemiological trends related to the age of patients and the diagnostic methods were analysed.

Results

Among 14 761 RSV tests, the overall number of positive tests for infants until 1 year of age peaked on 5 November 2022 (67 per 7 days) whereas it peaked on 22 December 2022 for adults (33 per 7 days). Positive antigen tests peaked on 7 November 2022 (56 per 7 days) whereas positive PCRs peaked on 19 December 2022 (36 per 7 days). Nevertheless, the positivity rate of RSV PCRs had peaked 1 month previously. Infants were mainly diagnosed through antigen testing, contrary to older patients. The influenza epidemic was probably the cause of the increased use of a quadruplex PCR, leading to a delayed increase in the absolute number of PCRs positive for RSV.

Conclusion

This study shows that the use of different diagnostic methods could lead to an erroneous representation of RSV epidemiology in adults due to the lack of sensitivity of antigen detection. RSV surveillance in the elderly should rely rather on molecular methods.

Genomic Analysis of Influenza A and B Viruses Carrying Baloxavir Resistance-Associated Substitutions Serially Passaged in Human Epithelial Cells

Baloxavir marboxil (baloxavir) is an FDA-approved inhibitor of the influenza virus polymerase acidic (PA) protein. Here, we used next-generation sequencing to compare the genomic mutational profiles of IAV H1N1 and H3N2, and IBV wild type (WT) and mutants (MUT) viruses carrying baloxavir resistance-associated substitutions (H1N1-PA I38L, I38T, and E199D; H3N2-PA I38T; and IBV-PA I38T) during passaging in normal human bronchial epithelial (NHBE) cells. We determined the ratio of nonsynonymous to synonymous nucleotide mutations (dN/dS) and identified the location and type of amino acid (AA) substitutions that occurred at a frequency of ≥30%. We observed that IAV H1N1 WT and MUT viruses remained relatively stable during passaging. While the mutational profiles for IAV H1N1 I38L, I38T, and E199D, and IBV I38T MUTs were relatively similar after each passage compared to the respective WTs, the mutational profile of the IAV H3N2 I38T MUT was significantly different for most genes compared to H3N2 WT. Our work provides insight into how baloxavir resistance-associated substitutions may impact influenza virus evolution in natural settings. Further characterization of the potentially adaptive mutations identified in this study is needed.

Impact of Baloxavir Resistance-Associated Substitutions on Influenza Virus Growth and Drug Susceptibility

Baloxavir marboxil (baloxavir) is a recently FDA-approved influenza virus polymerase acidic (PA) endonuclease inhibitor. Several PA substitutions have been demonstrated to confer reduced susceptibility to baloxavir; however, their impacts on measurements of antiviral drug susceptibility and replication capacity when present as a fraction of the viral population have not been established. We generated recombinant A/California/04/09 (H1N1)-like viruses (IAV) with PA I38L, I38T, or E199D substitutions and B/Victoria/504/2000-like virus (IBV) with PA I38T. These substitutions reduced baloxavir susceptibility by 15.3-, 72.3-, 5.4-, and 54.5-fold, respectively, when tested in normal human bronchial epithelial (NHBE) cells. We then assessed the replication kinetics, polymerase activity, and baloxavir susceptibility of the wild-type:mutant (WT:MUT) virus mixtures in NHBE cells. The percentage of MUT relative to WT virus necessary to detect reduced baloxavir susceptibility in phenotypic assays ranged from 10% (IBV I38T) to 92% (IAV E199D). While I38T did not alter IAV replication kinetics or polymerase activity, IAV PA I38L and E199D MUTs and the IBV PA I38T MUT exhibited reduced replication levels and significantly altered polymerase activity. Differences in replication were detectable when the MUTs comprised ≥90%, ≥90%, or ≥75% of the population, respectively. Droplet digital PCR (ddPCR) and next-generation sequencing (NGS) analyses showed that WT viruses generally outcompeted the respective MUTs after multiple replication cycles and serial passaging in NHBE cells when initial mixtures contained ≥50% of the WT viruses; however, we also identified potential compensatory substitutions (IAV PA D394N and IBV PA E329G) that emerged and appeared to improve the replication capacity of baloxavir-resistant virus in cell culture. IMPORTANCE Baloxavir marboxil, an influenza virus polymerase acidic endonuclease inhibitor, represents a recently approved new class of influenza antivirals. Treatment-emergent resistance to baloxavir has been observed in clinical trials, and the potential spread of resistant variants could diminish baloxavir effectiveness. Here, we report the impact of the proportion of drug-resistant subpopulations on the ability to detect resistance in clinical isolates and the impact of substitutions on viral replication of mixtures containing both drug-sensitive and drug-resistant variants. We also show that ddPCR and NGS methods can be successfully used for detection of resistant subpopulations in clinical isolates and to quantify their relative abundance. Taken together, our data shed light on the potential impact of baloxavir-resistant I38T/L and E199D substitutions on baloxavir susceptibility and other biological properties of influenza virus and the ability to detect resistance in phenotypic and genotypic assays.

Establishing Self-Harm Registers: The Role of Process Mapping to Improve Quality of Surveillance Data Globally

Self-harm registers (SHRs) are an essential means of monitoring rates of self-harm and evaluating preventative interventions, but few SHRs exist in countries with the highest burden of suicides and self-harm. Current international guidance on establishing SHRs recommends data collection from emergency departments, but this does not adequately consider differences in the provision of emergency care globally. We aim to demonstrate that process mapping can be used prior to the implementation of an SHR to understand differing hospital systems. This information can be used to determine the method by which patients meeting the SHR inclusion criteria can be most reliably identified, and how to mitigate hospital processes that may introduce selection bias into these data. We illustrate this by sharing in detail the experiences from a government hospital and non-profit hospital in south India. We followed a five-phase process mapping approach developed for healthcare settings during 2019-2020. Emergency care provided in the government hospital was accessed through casualty department triage. The non-profit hospital had an emergency department. Both hospitals had open access outpatient departments. SHR inclusion criteria overlapped with conditions requiring Indian medicolegal registration. Medicolegal registers are the most likely single point to record patients meeting the SHR inclusion criteria from multiple emergency care areas in India (e.g., emergency department/casualty, outpatients, other hospital areas), but should be cross-checked against registers of presentations to the emergency department/casualty to capture less-sick patients and misclassified cases. Process mapping is an easily reproducible method that can be used prior to the implementation of an SHR to understand differing hospital systems. This information is pivotal to choosing which hospital record systems should be used for identifying patients and to proactively reduce bias in SHR data. The method is equally applicable in low-, middle- and high-income countries.

An optimized cell-based assay to assess influenza virus replication by measuring neuraminidase activity and its applications for virological surveillance

Year-round virological characterization of circulating epidemic influenza viruses is conducted worldwide to detect the emergence of viruses that may escape pre-existing immunity or acquire resistance to antivirals. High throughput phenotypic assays are needed to complement the sequence-based analysis of circulating viruses and improve pandemic preparedness. The recent entry of a polymerase inhibitor, baloxavir, into the global market further highlighted this need. Here, we optimized a cell-based assay that considerably streamlines antiviral and antigenic testing by replacing lengthy immunostaining and imaging procedures used in current assay with measuring the enzymatic activity of nascent neuraminidase (NA) molecules expressed on the surface of virus-infected cells. For convenience, this new assay was named IRINA (Influenza Replication Inhibition Neuraminidase-based Assay). IRINA was successfully validated to assess inhibitory activity of baloxavir on virus replication by testing a large set (>150) of influenza A and B viruses, including drug resistant strains and viruses collected during 2017-2022. To test its versatility, IRINA was utilized to evaluate neutralization activity of a broadly reactive human anti-HA monoclonal antibody, FI6, and post-infection ferret antisera, as well as the inhibition of NA enzyme activity by NA inhibitors. Performance of IRINA was tested in parallel using respective conventional assays. IRINA offers an attractive alternative to current phenotypic assays, while maintaining reproducibility and high throughput capacity. Additionally, the improved turnaround time may prove to be advantageous when conducting time sensitive studies, such as investigating a new virus outbreak. This assay can meet the needs of surveillance laboratories by providing a streamlined and cost-effective approach for virus characterization.

Reciprocal relationships among influenza experiences, perceptions, and behavior: Results from a national, longitudinal survey of United States adults

OBJECTIVE

Our objective was to model the reciprocal relationships of perceived risk of contracting influenza with and without influenza vaccination, vaccination behavior, and reported influenza illness.

METHODS

We fit structural equation models to data from a longitudinal survey of adults in the United States collected through the RAND American Life Panel. Data come from fall and spring surveys fielded before and after each of 3 influenza seasons, 2016/2017, 2017/2018, and 2018/2019, for a total of 6 waves.

RESULTS

As expected, reported influenza experience was associated with increased perceived influenza risk in subsequent survey waves. Furthermore, perceived risk was associated with subsequent vaccination behavior, such that vaccination was more common for those with higher perceived unvaccinated influenza risk and lower perceived vaccinated influenza risk. Perhaps surprisingly, both elements of perceived risk were also associated with a greater likelihood of subsequent reported influenza illness. This malleability in illness reports may reflect uncertainty, as more respondents reported being sick but being unsure about whether they had influenza than reported certainty that they had influenza.

CONCLUSIONS

Interventions that influence perceptions about past experience with influenza, including increased testing and informational campaigns about influenza symptoms, could have unanticipated impacts on perceptions of influenza vaccination and vaccination behavior.

Burden of severe illness associated with laboratory confirmed influenza in adults aged 50-64 years: A rapid review

BACKGROUND

While the high burden of illness caused by seasonal influenza in children and the elderly is well recognize, less is known about the burden in adults 50-64 years of age. The lack of data for this age group is a key challenge in evaluating the cost-effectiveness of immunization programs. We aimed to assess influenza-associated hospitalization and mortality rates and case fatality rates for hospitalized cases among adults aged 50-64 years.

METHODS

This rapid review was conducted according to the PRISMA; we searched MEDLINE, EMBASE, Cochrane, Web of Science, and grey literature for articles and reports published since 2010. Studies reporting rates of hospitalization and/or mortality associated with laboratory-confirmed influenza among adults 50-64 or 45-64 years of age for the 2010-11 through 2019-20 seasons were included.

RESULTS

Twenty studies from 13 countries were reviewed. Reported rates of hospitalization associated with laboratory-confirmed influenza were 5.7 to 112.8 per 100,000. Rates tended to be higher in the 2015-2019 compared with the 2010-2014 seasons and were higher in studies reporting data from high-income versus low and middle-income countries. Mortality rates were reported in only one study, with rates ranging from 0.8 to 3.5 per 100,000 in four different seasons. The case fatality rate among those hospitalized with influenza, as reported by population-based studies, ranged from 1.3% to 5.6%.

CONCLUSIONS

Seasonal influenza imposes a significant burden of morbidity on adults 50-64 years of age but with high heterogeneity across seasons and geographic regions. Ongoing surveillance is required to improve estimates of burden to better inform influenza vaccination and other public health policies.

Cluster of Oseltamivir-Resistant and Hemagglutinin Antigenically Drifted Influenza A(H1N1)pdm09 Viruses, Texas, USA, January 2020

Four cases of oseltamivir-resistant influenza A(H1N1)pdm09 virus infection were detected among inhabitants of a border detention center in Texas, USA. Hemagglutinin of these viruses belongs to 6B.1A5A-156K subclade, which may enable viral escape from preexisting immunity. Our finding highlights the necessity to monitor both drug resistance and antigenic drift of circulating viruses.

Substantial effect of phytochemical constituents against the pandemic disease influenza-a review

Background

Influenza is an acute respiratory tract infection caused by the influenza virus. Vaccination and antiviral drugs are the two methods opted to control the disease. Besides their efficiency, they also cause adverse side effects. Hence, scientists turned their attention to powerful herbal medicines. This review put focus on various proven, scientifically validated anti-influenza compounds produced by the plants suggested for the production of newer drugs for the better treatment of influenza and its related antiviral diseases too.

Main body

In this review, fifty medicinal herb phytochemical constituents and their anti-influenza activities have been documented. Specifically, this review brings out the accurate and substantiates mechanisms of action of these constituents. This study categorizes the phytochemical constituents into primary and secondary metabolites which provide a source for synthesizing and developing new drugs.

Conclusion

This article provides a summary of the actions of the herbal constituents. Since the mechanisms of action of the components are elucidated, the pandemic situation arising due to influenza and similar antiviral diseases can be handled promisingly with greater efficiency. However, clinical trials are in great demand. The formulation of usage may be a single drug compound or multi-herbal combination. These, in turn, open up a new arena for the pharmaceutical industries to develop innovative drugs.

Process mapping in healthcare: a systematic review

INTRODUCTION

Process mapping (PM) supports better understanding of complex systems and adaptation of improvement interventions to their local context. However, there is little research on its use in healthcare. This study (i) proposes a conceptual framework outlining quality criteria to guide the effective implementation, evaluation and reporting of PM in healthcare; (ii) reviews published PM cases to identify context and quality of PM application, and the reported benefits of using PM in healthcare.

METHODS

We developed the conceptual framework by reviewing methodological guidance on PM and empirical literature on its use in healthcare improvement interventions. We conducted a systematic review of empirical literature using PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) methodology. Inclusion criteria were: full text empirical study; describing the process through which PM has been applied in a healthcare setting; published in English. Databases searched are: Medline, Embase, HMIC-Health Management Information Consortium, CINAHL-Cumulative Index to Nursing and Allied Health Literature, Scopus. Two independent reviewers extracted and analysed data. Each manuscript underwent line by line coding. The conceptual framework was used to evaluate adherence of empirical studies to the identified PM quality criteria. Context in which PM is used and benefits of using PM were coded using an inductive thematic analysis approach.

RESULTS

The framework outlines quality criteria for each PM phase: (i) preparation, planning and process identification, (ii) data and information gathering, (iii) process map generation, (iv) analysis, (v) taking it forward. PM is used in a variety of settings and approaches to improvement. None of the reviewed studies (N = 105) met all ten quality criteria; 7% were compliant with 8/10 or 9/10 criteria. 45% of studies reported that PM was generated through multi-professional meetings and 15% reported patient involvement. Studies highlighted the value of PM in navigating the complexity characterising healthcare improvement interventions.

CONCLUSION

The full potential of PM is inhibited by variance in reporting and poor adherence to underpinning principles. Greater rigour in the application of the method is required. We encourage the use and further development of the proposed framework to support training, application and reporting of PM.

TRIAL REGISTRATION

Prospero ID: CRD42017082140.

Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir

Pimodivir exerts an antiviral effect on the early stages of influenza A virus replication by inhibiting the cap-binding function of polymerase basic protein 2 (PB2). In this study, we used a combination of sequence analysis and phenotypic methods to evaluate pimodivir susceptibility of influenza A viruses collected from humans and other hosts. Screening PB2 sequences for substitutions previously associated with reduced pimodivir susceptibility revealed a very low frequency among seasonal viruses circulating in the U.S. during 2015–2020 (<0.03%; 3/11,934) and among non-seasonal viruses collected in various countries during the same period (0.2%; 18/8971). Pimodivir potently inhibited virus replication in two assays, a single-cycle HINT and a multi-cycle FRA, with IC₅₀ values in a nanomolar range. Median IC₅₀ values determined by HINT were similar for both subtypes of seasonal viruses, A(H1N1)pdm09 and A(H3N2), across three seasons. Human seasonal viruses with PB2 substitutions S324C, S324R, or N510K displayed a 27–317-fold reduced pimodivir susceptibility by HINT. In addition, pimodivir was effective at inhibiting replication of a diverse group of animal-origin viruses that have pandemic potential, including avian viruses of A(H5N6) and A(H7N9) subtypes. A rare PB2 substitution H357N was identified in an A(H4N2) subtype poultry virus that displayed >100-fold reduced pimodivir susceptibility. Our findings demonstrate a broad inhibitory activity of pimodivir and expand the existing knowledge of amino acid substitutions that can reduce susceptibility to this investigational antiviral.

The Seattle Flu Study: a multiarm community-based prospective study protocol for assessing influenza prevalence, transmission and genomic epidemiology

INTRODUCTION

Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect, characterise, and potentially contain new and emerging influenza strains at both an individual and population level. The objective of this study is to use data gathered simultaneously from community and hospital sites to develop a model of how influenza enters and spreads in a population.

METHODS AND ANALYSIS

Starting in the 2018-2019 season, we have been enrolling individuals with acute respiratory illness from community sites throughout the Seattle metropolitan area, including clinics, childcare facilities, Seattle-Tacoma International Airport, workplaces, college campuses and homeless shelters. At these sites, we collect clinical data and mid-nasal swabs from individuals with at least two acute respiratory symptoms. Additionally, we collect residual nasal swabs and data from individuals who seek care for respiratory symptoms at four regional hospitals. Samples are tested using a multiplex molecular assay, and influenza whole genome sequencing is performed for samples with influenza detected. Geospatial mapping and computational modelling platforms are in development to characterise the regional spread of influenza and other respiratory pathogens.

ETHICS AND DISSEMINATION

The study was approved by the University of Washington's Institutional Review Board (STUDY00006181). Results will be disseminated through talks at conferences, peer-reviewed publications and on the study website (www.seattleflu.org).

Detection of baloxavir resistant influenza A viruses using next generation sequencing and pyrosequencing methods

Baloxavir, a new antiviral drug targeting cap-dependent endonuclease activity of polymerase acidic (PA) protein of influenza viruses, is now approved in multiple countries. Several substitutions at isoleucine 38 in PA protein (e.g., PA-I38T) have been associated with decreased baloxavir susceptibility in vitro and in vivo. In recent years, next generation sequencing (NGS) analysis and pyrosequencing have been used by CDC and U.S. Public Health Laboratories to monitor drug susceptibility of influenza viruses. Here we described an improved pyrosequencing assay for detecting influenza A viruses carrying substitutions at PA-38. Cyclic and customized orders of nucleotide dispensation were evaluated, and pyrosequencing results were compared to those generated using NGS. Our data showed that the customized nucleotide dispensation has improved the pyrosequencing assay performance in identification of double mixtures (e.g., PA-38I/T); however, identification of PA-38 variants in triple mixtures remains a challenge. While NGS analysis indicated the presence of PA-I38K in one clinical specimen and isolate, our attempts to detect this mutation by pyrosequencing or recover the virus carrying PA-I38K in cell culture were unsuccessful, raising a possibility of a rarely occurring sequencing error. Overall, pyrosequencing provides a convenient means to detect baloxavir resistant influenza viruses when NGS is unavailable or a faster turnaround time is required.

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Pyrosequencing assay was optimized to improve detection of baloxavir resistant influenza A viruses in mixtures.

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Detection of PA-38 variants in virus mixtures of both subtypes was improved by using customized nucleotide dispensation.

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Pyrosequencing and NGS data were comparable, except for lysine at PA-38 that was detected by NGS but not by pyrosequencing.

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Attempts to recover virus carrying lysine at PA-38 were unsuccessful, raising the rare possibility of an NGS artifact.

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Pyrosequencing provides an important addition to genotypic methods that can be used for baloxavir susceptibility testing.

Application of volumetric absorptive microsampling (VAMS) to measure multidimensional anti-influenza IgG antibodies by the mPlex-Flu assay

Introduction: Recently, volumetric absorptive microsampling (VAMS) has been used for accurate sampling of a fixed peripheral blood volume (10 µL) on a volumetric swab, and long-term sample storage. The mPlex-Flu assay is a novel, high-throughput assay that simultaneously measures the concentration of antibodies against the hemagglutinin (HA) proteins from multiple influenza virus strains with ≤5 µL of serum. Here we describe combining these two methods to measure multidimensional anti-influenza IgG activity in whole blood samples collected by a finger stick and VAMS, with correction for serum volume based on simultaneous hemoglobin measurement. Methods: We compared capillary blood samples obtained from a finger stick using a VAMS device with serum samples collected by traditional phlebotomy from 20 subjects, with the influenza antibody profiles measured by the mPlex-Flu assay. Results: We found that results with the two sampling methods were highly correlated within subjects and across all influenza strains (mean R 2 = 0.9470). Adjustment for serum volume, based on hemaglobin measurement, was used to estimate serum volume of samples and improved the accuracy. IgG measurements were stable over 3 weeks when VAMS samples were stored at room temperature or transported using a variety of shipping methods. Additionally, when volunteers performed finger-stick VAMS at-home by themselves, the comparison results of anti-HA antibody concentrations were highly consistent with sampling performed by study personnel on-site (R 2 = 0.9496). Conclusions: This novel approach can provide a simple, accurate, and low-cost means for monitoring the IgG anti-influenza HA antibody responses in large population studies and clinical trials.

New York State Emergency Preparedness and Response to Influenza Pandemics 1918-2018

Emergency health preparedness and response efforts are a necessity in order to safeguard the public against major events, such as influenza pandemics. Since posting warnings of the epidemic influenza in 1918, to the mass media communications available a century later, state, national and global public health agencies have developed sophisticated networks, tools, detection methods, and preparedness plans. These progressive measures guide health departments and clinical providers, track patient specimens and test reports, monitor the spread of disease, and evaluate the most threatening influenza strains by means of risk assessment, to be able to respond readily to a pandemic. Surge drills and staff training were key aspects for New York State preparedness and response to the 2009 influenza pandemic, and the re-evaluation of preparedness plans is recommended to ensure readiness to address the emergence and spread of a future novel virulent influenza strain.

FluChip-8G Insight: HA and NA subtyping of potentially pandemic influenza A viruses in a single assay

BACKGROUND

Global influenza surveillance in humans and animals is a critical component of pandemic preparedness. The FluChip-8G Insight assay was developed to subtype both seasonal and potentially pandemic influenza viruses in a single assay with a same day result. FluChip-8G Insight uses whole gene segment RT-PCR-based amplification to provide robustness against genetic drift and subsequent microarray detection with artificial neural network-based data interpretation.

OBJECTIVES

The objective of this study was to verify and validate the performance of the FluChip-8G Insight assay for the detection and positive identification of human and animal origin non-seasonal influenza A specimens.

METHODS

We evaluated the ability of the FluChip-8G Insight technology to type and HA and NA subtype a sample set consisting of 297 results from 180 unique non-seasonal influenza A strains (49 unique subtypes).

RESULTS

FluChip-8G Insight demonstrated a positive percent agreement ≥93% for 5 targeted HA and 5 targeted NA subtypes except for H9 (88%), and negative percent agreement exceeding 95% for all targeted subtypes.

CONCLUSIONS

The FluChip-8G Insight neural network-based algorithm used for virus identification performed well over a data set of 297 naïve sample results, and can be easily updated to improve performance on emerging strains without changing the underlying assay chemistry.

Analytical evaluation of the microarray-based FluChip-8G Influenza A+B Assay

BACKGROUND

Influenza causes a significant annual disease burden, with characterization of the infecting virus important in clinical and public health settings. Rapid immunoassays are fast but insensitive, whereas real-time RT-PCR is sensitive but susceptible to genetic mutations and often requires multiple serial assays. The FluChip-8G Influenza A+B Assay provides type and subtype/lineage identification of influenza A and B, including non-seasonal A viruses, in a single microarray-based assay with same day turnaround time.

OBJECTIVE

To evaluate key analytical performance characteristics of the FluChip-8G Influenza A+B Assay.

STUDY DESIGN

Analytical sensitivity, cross-reactivity, and multi-site reproducibility were evaluated.

RESULTS

The limit of detection (LOD) for the FluChip-8G influenza A+B Assay ranged from 5.8 × 10²-1.5 × 10⁵ genome copies/mL, with most samples ∼2 × 10³ genome copies/mL (∼160 genome copies/reaction). Fifty two (52) additional strains were correctly identified near the LOD, demonstrating robust reactivity. Two variant viruses (H1N1v and H3N2v) resulted in dual identification as both "non-seasonal influenza A" and A/H1N1pdm09. No reproducible cross-reactivity was observed for the 34 organisms tested, however, challenges with internal control inhibition due to crude growth matrix were observed. Lastly, samples tested near the LOD showed high reproducibility (97.0% (95% CI 94.7-98.7)) regardless of operator, site, reagent lot, or testing day.

CONCLUSION

The FluChip-8G Influenza A+B Assay is an effective new method for detecting and identifying both seasonal and non-seasonal influenza viruses, as revealed by good sensitivity and robust reactivity to 52 unique strains of influenza virus. In addition, the lack of cross-reactivity to non-influenza pathogens and high lab-to-lab reproducibility highlight the analytical performance of the assay as an alternative to real-time RT-PCR and sequencing-based assays. Clinical validation of the technology in a multi-site clinical study is the subject of a separate investigation.

Assessing baloxavir susceptibility of influenza viruses circulating in the United States during the 2016/17 and 2017/18 seasons

The anti-influenza therapeutic baloxavir targets cap-dependent endonuclease activity of polymerase acidic (PA) protein. We monitored baloxavir susceptibility in the United States with next generation sequencing analysis supplemented by phenotypic one-cycle infection assay. Analysis of PA sequences of 6,891 influenza A and B viruses collected during 2016/17 and 2017/18 seasons showed amino acid substitutions: I38L (two A(H1N1)pdm09 viruses), E23G (two A(H1N1)pdm09 viruses) and I38M (one A(H3N2) virus); conferring 4-10-fold reduced susceptibility to baloxavir.

Estimating Vaccine-Driven Selection in Seasonal Influenza

Vaccination could be an evolutionary pressure on seasonal influenza if vaccines reduce the transmission rates of some ("targeted") strains more than others. In theory, more vaccinated populations should have a lower prevalence of targeted strains compared to less vaccinated populations. We tested for vaccine-induced selection in influenza by comparing strain frequencies between more and less vaccinated human populations. We defined strains in three ways: first as influenza types and subtypes, next as lineages of type B, and finally as clades of influenza A/H3N2. We detected spatial differences partially consistent with vaccine use in the frequencies of subtypes and types and between the lineages of influenza B, suggesting that vaccines do not select strongly among all these phylogenetic groups at regional scales. We did detect a significantly greater frequency of an H3N2 clade with known vaccine escape mutations in more vaccinated countries during the 2014⁻2015 season, which is consistent with vaccine-driven selection within the H3N2 subtype. Overall, we find more support for vaccine-driven selection when large differences in vaccine effectiveness suggest a strong effect size. Variation in surveillance practices across countries could obscure signals of selection, especially when strain-specific differences in vaccine effectiveness are small. Further examination of the influenza vaccine's evolutionary effects would benefit from improvements in epidemiological surveillance and reporting.