Detecting 2009 pandemic influenza A (H1N1) virus infection: availability of diagnostic testing led to rapid pandemic response

High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment

A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.

Pivot, persevere, or perish: how Ellume Health overcame development and regulatory obstacles to become the first authorized over-the-counter COVID-19 test in the United States

The Ellume COVID-19 home test from Ellume Health (Brisbane, Aus) became the first COVID-19 diagnostic tool authorized for home use by the United States FDA in December 2020. This early pandemic success was built on over ten years of work on the Ellume influenza home test. Ellume overcame critical technology challenges during the development of their influenza test. In addition, it faced a recall of its COVID-19 home test in 2021 due to false positive results. While Ellume initially persevered through the recall and restarted sales in the United States, the combination of the recall and the wide availability of competitors' low-cost over the counter tests in the United States led to Ellume entering voluntary administration in September 2022. This paper traces the history of Ellume and how 10 years of experience with a home influenza test allowed the company to quickly develop the Ellume COVID-19 home test. We will also provide to diagnostic developers the key strategies employed by Ellume to succeed while highlighting the pitfalls that have challenged the company's business success.

Effectiveness of Influenza Vaccination of Pregnant Women for Prevention of Maternal and Early Infant Influenza-Associated Hospitalizations in South Africa: A Prospective Test-Negative Study

BACKGROUND

Influenza vaccination during pregnancy reduces influenza-associated illness in the women and their infants, but effectiveness estimates against influenza-associated hospitalization are limited and lacking from settings with high human immunodeficiency virus (HIV) infection prevalence. We assessed the effect of maternal vaccination in HIV-uninfected women and women with HIV in preventing influenza-associated hospitalizations in infants and the women.

METHODS

During 2015-2018, influenza vaccination campaigns targeting pregnant women were augmented at selected antenatal clinics; these were coupled with prospective hospital-based surveillance for acute respiratory or febrile illness in infants aged <6 months and cardiorespiratory illness among pregnant or postpartum women. Vaccine effectiveness (VE) was assessed using a test-negative case-control study.

RESULTS

Overall, 71 influenza-positive and 371 influenza-negative infants were included in the analysis; mothers of 26.8% of influenza-positive infants were vaccinated during pregnancy compared with 35.6% of influenza-negative infants, corresponding to an adjusted VE (aVE) of 29.0% (95% confidence interval [CI], -33.6% to 62.3%). When limited to vaccine-matched strains, aVE was 65.2% (95% CI, 11.7%-86.3%). For maternal hospitalizations, 56 influenza-positive and 345 influenza-negative women were included in the analysis, with 28.6% of influenza-positive women being vaccinated compared with 38.3% of influenza-negatives, for an aVE of 46.9% (95% CI, -2.8% to 72.5%). Analysis restricted to HIV-uninfected women resulted in 82.8% (95% CI, 40.7%-95.0%) aVE. No significant aVE (-32.5% [95% CI, -208.7% to 43.1%]) was detected among women with HIV.

CONCLUSIONS

Influenza vaccination during pregnancy prevented influenza-associated hospitalizations among young infants when infected with vaccine strains and among HIV-uninfected women.

Useful clinical findings and simple laboratory data for the diagnosis of seasonal influenza

BACKGROUND

When using rapid antigen test kits for the diagnosis of influenza, false-negative results may occur if done too soon after the onset of symptoms. The purpose of this study was done to determine clinical laboratory items other than rapid antigen testing are useful for diagnosing influenza.

METHODS

The subjects were 915 patients who visited the outpatient clinic of hospital between April 2010 and March 2017 during the influenza epidemic seasons, from December to April, and had both fever of 37.0 degrees or more and cold symptoms.

RESULTS

Of the 214 patients who met the inclusion criteria, 176 had influenza. Multivariate analysis extracted patient consultation within four days of onset, fever of 37 degrees or higher, posterior pharyngeal lymphoid follicles, CRP of 0.77 mg/dL or less, and a lymphocyte count of 900/μL less as independent variables.

CONCLUSION

In previous study, lymphoid follicles on the posterior pharyngeal wall and decreased lymphocyte count were reported as influenza-specific findings. Both were confirmed with high specificity in our study, indicating that both would be useful when patients with influenza-like symptoms were false-negative for the rapid antigen test.

Cohort profile: A Prospective Household cohort study of Influenza, Respiratory syncytial virus and other respiratory pathogens community burden and Transmission dynamics in South Africa, 2016-2018

Purpose

The PHIRST study (Prospective Household cohort study of Influenza, Respiratory Syncytial virus, and other respiratory pathogens community burden and Transmission dynamics in South Africa) aimed to estimate the community burden of influenza and respiratory syncytial virus (RSV) including the incidence of infection, symptomatic fraction, and to assess household transmission.

Participants

We enrolled 1684 individuals in 327 randomly selected households in a rural and an urban site over three consecutive influenza and two RSV seasons. A new cohort of households was enrolled each year. Participants were sampled with nasopharyngeal swabs twice‐weekly during the RSV and influenza seasons of the year of enrolment. Serology samples were collected at enrolment and before and after the influenza season annually.

Findings to Date

There were 122 113 potential individual follow‐up visits over the 3 years, and participants were interviewed for 105 783 (87%) of these. Out of 105 683 nasopharyngeal swabs, 1258 (1%) and 1026 (1%) tested positive on polymerase chain reaction (PCR) for influenza viruses and RSV, respectively. Over one third of individuals had PCR‐confirmed influenza each year. Overall, there was influenza transmission to 10% of household contacts of an index case.

Future Plans

Future planned analyses include analysis of influenza serology results and RSV burden and transmission. Households enrolled in the PHIRST study during 2016–2018 were eligible for inclusion in a study of SARS‐CoV‐2 transmission initiated in July 2020. This study uses similar testing frequency to assess the community burden of SARS‐CoV‐2 infection and the role of asymptomatic infection in virus transmission.

RNA Engineering for Public Health: Innovations in RNA-Based Diagnostics and Therapeutics

RNA is essential for cellular function: From sensing intra- and extracellular signals to controlling gene expression, RNA mediates a diverse and expansive list of molecular processes. A long-standing goal of synthetic biology has been to develop RNA engineering principles that can be used to harness and reprogram these RNA-mediated processes to engineer biological systems to solve pressing global challenges. Recent advances in the field of RNA engineering are bringing this to fruition, enabling the creation of RNA-based tools to combat some of the most urgent public health crises. Specifically, new diagnostics using engineered RNAs are able to detect both pathogens and chemicals while generating an easily detectable fluorescent signal as an indicator. New classes of vaccines and therapeutics are also using engineered RNAs to target a wide range of genetic and pathogenic diseases. Here, we discuss the recent breakthroughs in RNA engineering enabling these innovations and examine how advances in RNA design promise to accelerate the impact of engineered RNA systems.

Epidemiological and clinical characteristics of community-acquired and nosocomial influenza cases and risk factors associated with complications: A four season analysis of all adult patients admitted in a tertiary hospital

Background

Information on the characteristics of patients with nosocomial influenza and associated complications is scarce. This study compared epidemiological and clinical characteristics of patients admitted with hospital‐acquired influenza (HAI) to those with community‐acquired influenza (CAI) and analyzed risk factors associated with complications.

Methods

This retrospective, observational study included all adult patients with confirmed influenza virus infection admitted to Son Espases University Hospital during the influenza season in Spain (October to May) from 2012‐2013 to 2015‐2016. Symptom onset before admission was included as CAI, and 2 days after admission or within 48 hours after previous discharge were considered as HAI.

Results

Overall, 666 patients with laboratory‐confirmed influenza were included; 590 (88.6%) and 76 (11.4%) had CAI and HAI, respectively. Baseline characteristics and vaccination rates were similar in both groups. Patients with HAI had significantly fewer symptoms, less radiological alterations, and earlier microbiological diagnosis than those with CAI. Eighty‐five (14.4%) and 20 (27.6%) CAI and HAI patients, respectively, experienced at least one complication, including septic shock, admission to the intensive care unit, mechanical ventilation or evolution to death (any one, P = .003). Univariate and multivariate binary logistic regression was performed to assess independent risk factors associated with the occurrence of complications: nosocomial infection, diabetes, oseltamivir treatment, having received no vaccination, microbiological delay, dyspnea, and the state of confusion were the most important significant factors.

Conclusions

Our study shows the need to implement microbiological diagnostic measures in the first 48 hours to reduce HAI frequency and associated complications.

Is "no test is better than a bad test"? Impact of diagnostic uncertainty in mass testing on the spread of COVID-19

Testing is viewed as a critical aspect of any strategy to tackle epidemics. Much of the dialogue around testing has concentrated on how countries can scale up capacity, but the uncertainty in testing has not received nearly as much attention beyond asking if a test is accurate enough to be used. Even for highly accurate tests, false positives and false negatives will accumulate as mass testing strategies are employed under pressure, and these misdiagnoses could have major implications on the ability of governments to suppress the virus. The present analysis uses a modified SIR model to understand the implication and magnitude of misdiagnosis in the context of ending lockdown measures. The results indicate that increased testing capacity alone will not provide a solution to lockdown measures. The progression of the epidemic and peak infections is shown to depend heavily on test characteristics, test targeting, and prevalence of the infection. Antibody based immunity passports are rejected as a solution to ending lockdown, as they can put the population at risk if poorly targeted. Similarly, mass screening for active viral infection may only be beneficial if it can be sufficiently well targeted, otherwise reliance on this approach for protection of the population can again put them at risk. A well targeted active viral test combined with a slow release rate is a viable strategy for continuous suppression of the virus.

Comparative epidemiology between the 2009 H1N1 influenza and COVID-19 pandemics

In a short time, humanity has experienced two pandemics: the influenza A virus pandemic (pH1N1) in 2009 and the coronavirus disease 2019 (COVID-19) pandemic in 2020. Therefore, it is likely that the general population will erroneously seek to compare the two pandemics and adopt similar attitudes in facing them. However, the two pandemics have their intrinsic characteristics that distinguish them considerably; for example, the virulence of the infectious agents and the availability of treatment and vaccine. Consequently, given this knowledge gap between the pH1N1 and COVID-19 pandemics, we conducted this review to clarify and summarize, above all, the epidemiological historical aspects of these two viruses of great importance to global public health.

Responding to the Challenges of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Perspectives from the Association for Molecular Pathology Infectious Disease Subdivision Leadership

Clinical molecular laboratory professionals are at the frontline of the response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, providing accurate, high-quality laboratory results to aid in diagnosis, treatment, and epidemiology. In this role, we have encountered numerous regulatory, reimbursement, supply-chain, logistical, and systems challenges that we have struggled to overcome to fulfill our calling to provide patient care. In this Perspective from the Association for Molecular Pathology Infectious Disease Subdivision Leadership team, we review how our members have risen to these challenges, provide recommendations for managing the current pandemic, and outline the steps we can take as a community to better prepare for future pandemics.

Human surveillance and phylogeny of highly pathogenic avian influenza A(H5N8) during an outbreak in poultry in South Africa, 2017

Background

In June 2017, an outbreak of the highly pathogenic avian influenza A(H5N8) was detected in commercial poultry farms in South Africa, which rapidly spread to all nine South African provinces.

Objectives

We conducted active surveillance for the transmission of influenza A(H5N8) to humans working with infected birds during the South African outbreak.

Methods

Influenza A(H5N8)‐positive veterinary specimens were used to evaluate the ability of real‐time PCR‐based assays to detect contemporary avian influenza A(H5N8) strains. Whole genome sequences were generated from these specimens by next‐generation sequencing for phylogenetic characterization and screening for mammalian‐adaptive mutations.

Results

Human respiratory samples from 74 individuals meeting our case definition, all tested negative for avian influenza A(H5) by real‐time PCR, but 2 (3%) were positive for human influenza A(H3N2). 54% (40/74) reported wearing personal protective equipment including overalls, boots, gloves, masks, and goggles. 94% (59/63) of veterinary specimens positive for H5N8 were detected on an influenza A(H5) assay for human diagnostics. A commercial H5N8 assay detected H5 in only 6% (3/48) and N8 in 92% (44/48). Thirteen (13/25; 52%) A(H5N8) genomes generated from veterinary specimens clustered in a single monophyletic clade. These sequences contained the NS (P42S) and PB2 (L89V) mutations noted as markers of mammalian adaptation.

Conclusions

Diagnostic assays were able to detect and characterize influenza A(H5N8) viruses, but poor performance is reported for a commercial assay. Absence of influenza A(H5N8) in humans with occupational exposure and no clear impression of molecular adaptation for mammalian infection suggest that this avian pathogen continues to be low‐risk human pathogen.

Evaluation of the influenza sentinel surveillance system in the Democratic Republic of Congo, 2012-2015

BACKGROUND

The World Health Organization recommends periodic evaluations of influenza surveillance systems to identify areas for improvement and provide evidence of data reliability for policymaking. However, data about the performance of established influenza surveillance systems are limited in Africa, including in the Democratic Republic of Congo (DRC).

METHODS

We used the Centers for Disease Control and Prevention guidelines to evaluate the performance of the influenza sentinel surveillance system (ISSS) in DRC during 2012-2015. The performance of the system was evaluated using eight surveillance attributes: (i) data quality and completeness for key variables, (ii) timeliness, (iii) representativeness, (iv) flexibility, (v) simplicity, (vi) acceptability, (vii) stability and (viii) utility. For each attribute, specific indicators were developed and described using quantitative and qualitative methods. Scores for each indicator were as follows: < 60% weak performance; 60-79% moderate performance; ≥80% good performance.

RESULTS

During 2012-2015, we enrolled and tested 4339 patients with influenza-like illness (ILI) and 2869 patients with severe acute respiratory illness (SARI) from 11 sentinel sites situated in 5 of 11 provinces. Influenza viruses were detected in 446 (10.3%) samples from patients with ILI and in 151 (5.5%) samples from patients with SARI with higher detection during December-May. Data quality and completeness was > 90% for all evaluated indicators. Other strengths of the system were timeliness, simplicity, stability and utility that scored > 70% each. Representativeness, flexibility and acceptability had moderate performance. It was reported that the ISSS contributed to: (i) a better understanding of the epidemiology, circulating patterns and proportional contribution of influenza virus among patients with ILI or SARI; (ii) acquisition of new key competences related to influenza surveillance and diagnosis; and (iii) continuous education of surveillance staff and clinicians at sentinel sites about influenza. However, due to limited resources no actions were undertaken to mitigate the impact of seasonal influenza epidemics.

CONCLUSIONS

The system performed overall satisfactorily and provided reliable and timely data about influenza circulation in DRC. The simplicity of the system contributed to its stability. A better use of the available data could be made to inform and promote prevention interventions especially among the most vulnerable groups.

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.

Dynamic changes of lymphocyte counts in adult patients with severe pandemic H1N1 influenza A

Background

Lymphopenia has been observed in severe pandemic influenza A/H1N1 in developed countries. However, data from developing countries are rare and dynamic change of lymphocyte counts in severe pandemic influenza A/H1N1 is scarcely reported. This study aimed to observe change of lymphocyte counts in patients with severe pandemic influenza A/H1N1 and to investigate the correlation of lymphopenia and severe pandemic influenza A/H1N1.

Methods

We retrospectively analyzed the white blood cell counts and differentials and other clinical data in 21 hospitalized patients with severe pandemic influenza A/H1N1 confirmed by reverse-transcription PCR during 2009 and 2010.

Results

All patients, except two cases with bacterial co-infections, had normal or reduced white blood cell counts. Seventeen (81.0%) patients had decreased lymphocyte proportions (<20%) and counts (<0.8 × 10⁹/L), with the lowest value of 1.2% and 0.1 × 10⁹/L respectively. A patient with nosocomial infection of influenza A/H1N1 showed that lymphopenia occurred on the first day of illness. Lymphocyte proportions and absolute counts returned to normal or slightly higher than normal in 16 of the 17 patients within 2–3 weeks after the disease onset.

Conclusions

Lymphopenia along with other clinical parameters may be helpful in early differential diagnosis of severe pandemic influenza A/H1N1.

Outbreak of influenza A in a boarding school in South Africa, 2016

Introduction

We investigated an outbreak of influenza-like illness (ILI) at a boarding school in Eastern Cape Province, South Africa. We aimed to confirm the etiological agent, estimate attack rates and identify risk factors for illness.

Methods

We conducted a retrospective cohort study including senior school boarders (n=308). Students with ILI (cough and fever) were identified through school medical records. We also conducted a questionnaire-based cross-sectional study among senior students including boarders (n=107) and day students (n=45). We collected respiratory specimens for respiratory pathogen testing by real-time polymerase chain reaction from a subset of symptomatic students. We calculated attack rates of medically attended ILI (medILI) and identified factors associated with medILI using logistic regression. We calculated seasonal influenza vaccine effectiveness (VE) against medILI.

Results

Influenza A (H3N2) virus was detected in 61% (23/38) of specimens. Attack rate for medILI was 13% among boarders (39/308) in the cohort study and 20% in both day students (9/45) and boarders (21/107) in the cross-sectional study. Playing squash was associated with medILI (aOR 5.35, 95% confidence interval [95% CI]: 1.68-17.07). Of the boarders, 19% (57/308) were vaccinated before the outbreak. The adjusted VE against medILI was 18% (aOR 0.82, 95% CI 0.38-1.78). The outbreak led to cancellation of several events and the need for academic remedial sessions.

Conclusion

We confirmed an influenza A (H3N2) virus outbreak with a high attack rate. The outbreak affected academic and sports activities. Participation in sports and social gatherings while experiencing ILI should be discouraged to reduce viral transmission and impact on school activities.

Progress in Vaccine-Preventable and Respiratory Infectious Diseases-First 10 Years of the CDC National Center for Immunization and Respiratory Diseases, 2006-2015

The need for closer linkages between scientific and programmatic areas focused on addressing vaccine-preventable and acute respiratory infections led to establishment of the National Center for Immunization and Respiratory Diseases (NCIRD) at the Centers for Disease Control and Prevention. During its first 10 years (2006–2015), NCIRD worked with partners to improve preparedness and response to pandemic influenza and other emergent respiratory infections, provide an evidence base for addition of 7 newly recommended vaccines, and modernize vaccine distribution. Clinical tools were developed for improved conversations with parents, which helped sustain childhood immunization as a social norm. Coverage increased for vaccines to protect adolescents against pertussis, meningococcal meningitis, and human papillomavirus–associated cancers. NCIRD programs supported outbreak response for new respiratory pathogens and oversaw response of the Centers for Disease Control and Prevention to the 2009 influenza A(H1N1) pandemic. Other national public health institutes might also find closer linkages between epidemiology, laboratory, and immunization programs useful.

A novel PCR-based point-of-care method facilitates rapid, efficient, and sensitive diagnosis of influenza virus infection

OBJECTIVE

The aim of this single-centre study was the comparative analysis of the GeneXpert (Cepheid Inc.) and the LIAT (Roche) system for the rapid polymerase chain reaction (PCR)-based detection of influenza A (IA) and influenza B (IB) viruses.

PATIENTS AND METHODS

During the 2017-2018 flu season, 651 prospectively collected samples (throat and nasal swabs) of patients with symptoms of influenza-like illness or acute respiratory infection were tested for the presence of IA and IB viruses using the GeneXpert and LIAT systems. To evaluate the usefulness for near-patient testing, a LIAT system was installed at the Department of Emergency Medicine, and sample testing was performed on site. Reference testing of all samples was performed with the Xpert Flu assay and for 313 samples in addition with the Xpert Xpress Flu/RSV (respiratory syncytial virus) assay at the central laboratory. Analysis of all samples was carried out within 24 hr after collection.

RESULTS

Overall, 267 of the 651 samples analysed were positive for influenza viruses in at least one of the three assays investigated (IA, 88; IB, 179). The overall rates of agreement between the LIAT assay and the Xpert Flu assay was 96.0% for the detection of IA and IB viruses. The sensitivity and specificity of the LIAT assay compared to the Xpert Flu assay for the detection of IA was 98.80% (95% confidence interval (CI) 93.47-99.97%) and 99.12% (95% CI, 97.96% to 99.71%) and for the detection of IB 98.76% (95% CI 95.58-99.85%), and 96.33% (95% CI 94.26-97.81%), respectively. The LIAT assay showed a statistically significant higher detection rate of IB virus than the Xpert Flu assay (p <0.01). No significant difference was found between the detection rate of the LIAT assay and the Xpert Xpress Flu/RSV assay. The mean time to the availability of a definite test result was significantly shorter with the on-site LIAT system than the GeneXpert system (mean 59 min saving time; p <0.01).

CONCLUSION

The LIAT system represents a robust and highly sensitive point-of-care device for the rapid PCR-based detection of influenza A and influenza B viruses.

Readiness for Responding to a Severe Pandemic 100 Years After 1918

The 1918 H1N1 pandemic caused an unprecedented number of deaths worldwide. The tools to deal with the global emergency were limited; there were insufficient surveillance systems and a dearth of diagnostic, treatment, and prevention options. With continuing focus on pandemic planning, technologic advances in surveillance, vaccine capabilities, and 21st century medical care and countermeasures, we are more prepared for a severe pandemic than people were 100 years ago; however, notable gaps remain.

Replacement of neuraminidase inhibitor-susceptible influenza A(H1N1) with resistant phenotype in 2008 and circulation of susceptible influenza A and B viruses during 2009-2013, South Africa

Background

Data on the susceptibility of influenza viruses from South Africa to neuraminidase inhibitors (NAIs) are scarce, and no extensive analysis was done.

Objectives

We aimed to determine oseltamivir and zanamivir susceptibility of influenza A and B virus neuraminidases (NAs), 2007‐2013, South Africa.

Patients/Methods

We enrolled participants through national influenza‐like illness surveillance, 2007‐2013. Influenza diagnosis was by virus isolation and quantitative polymerase chain reaction (qPCR). Drug susceptibility was determined by chemiluminescence‐based NA‐STAR/NA‐XTD assay. Sanger sequencing was used to determine molecular markers of NAI resistance.

Results

Forty percent (6341/15 985) of participants were positive for influenza viruses using virus isolation (2007‐2009) and qPCR (2009‐2013) methods. A total of 1236/6341 (19.5%) virus isolates were generated of which 307/1236 (25%) were tested for drug susceptibility. During 2007‐2008, the median 50% inhibitory concentration (IC₅₀) of oseltamivir for seasonal influenza A(H1N1) increased from of 0.08 nmol/L (range 0.01‐3.60) in 2007 to 73 nmol/L (range 1.56‐305 nmol/L) in 2008. Influenza A isolates from 2009 to 2013 were susceptible to oseltamivir [A(H3N2) median IC₅₀ = 0.05 nmol/L (range 0.01‐0.08); A(H1N1)pdm09 = 0.11 nmol/L (range 0.01‐0.78)] and zanamivir [A(H3N2) median IC₅₀ = 0.56 nmol/L (range 0.47‐0.66); A(H1N1)pdm09 = 0.35 nmol/L (range 0.27‐0.533)]. Influenza B viruses were susceptible to both NAIs. NAI resistance‐associated substitutions H275Y, E119V, and R150K (N1 numbering) were not detected in influenza A viruses that circulated in 2009‐2013.

Conclusions

We confirm replacement of NAI susceptible by resistant phenotype influenza A(H1N1) in 2008. Influenza A and B viruses (2009‐2013) remained susceptible to NAIs; therefore, these drugs are useful for treating influenza‐infected patients.

Diagnostic Performance of Multiplex Nucleic Acid Testing of Bronchoalveolar Lavage and Bronchial Wash Specimens for Respiratory Viral Pathogens

There is limited knowledge on the yield of performing multiplex nucleic acid testing (NAT) on multiple lower respiratory tract specimens from a single patient with a single instance of infection. We evaluated the performance characteristics of multiplex NAT assays performed concurrently on bronchoalveolar lavage (BAL) and bronchial wash (BW) specimens to detect respiratory pathogens. A retrospective study of admitted patients from March 2013 through December 2016 was performed. Individual performance characteristics of BAL and BW specimens were compared to positive results from either set of specimens. Only contemporaneous BAL and BW specimens (received by the laboratory within 4 h of each other) were included. The final cohort included 170 patients, with 184 contemporaneous BAL and BW specimens submitted for multiplex NAT (median age, 58 years; 62% male). Of the patients with positive NAT results, 38 of 40 BW specimens tested positive (overall percent agreement with combined testing, 98.9%; 95% confidence interval [CI], 95.5 to 98.9%), and 34 of 40 BAL specimens tested positive (overall percent agreement with combined testing, 96.7%; 95% CI, 93.0 to 96.7%). Assays performed on BW specimens identified 4 additional specimens and had a higher positive percent agreement (95.0%) with combined testing results compared to those performed on BAL specimens (85.0%). There was exact concordance in 174 specimens (94.6%; negative and positive for respiratory pathogens, 144 and 34 specimens, respectively). We observed high concordance (95%) between multiplex NAT results from contemporaneous BAL and BW specimens. Performance characteristics of BW specimen testing were equivalent to those of BAL specimen testing. The benefit of performing additional testing should be carefully considered against the potential complications and health care costs.

Influenza Viral Shedding in a Prospective Cohort of HIV-Infected and Uninfected Children and Adults in 2 Provinces of South Africa, 2012-2014

Background

Prolonged shedding of influenza viruses may be associated with increased transmissibility and resistance mutation acquisition due to therapy. We compared duration and magnitude of influenza shedding between human immunodeficiency virus (HIV)-infected and -uninfected individuals.

Methods

A prospective cohort study during 3 influenza seasons enrolled patients with influenza-like illness and a positive influenza rapid test. Influenza viruses were detected by real-time reverse transcription polymerase chain reaction. Weibull accelerated failure time regression models were used to describe influenza virus shedding. Mann-Whitney U tests explored initial influenza viral loads (VL).

Results

Influenza virus shedding duration was similar in 65 HIV-infected (6 days; interquartile range [IQR] 3-10) and 176 HIV-uninfected individuals (7 days; IQR 4-11; P = .97), as was initial influenza VL (HIV-uninfected 5.28 ± 1.33 log10 copies/mL, HIV-infected 4.73 ± 1.68 log10 copies/mL; P = .08). Adjusted for age, HIV-infected individuals with low CD4 counts shed influenza virus for longer than those with higher counts (adjusted hazard ratio 3.55; 95% confidence interval, 1.05-12.08).

Discussion

A longer duration of influenza virus shedding in HIV-infected individuals with low CD4 counts may suggest a possible increased risk for transmission or viral evolution in severely immunocompromised individuals. HIV-infected individuals should be prioritized for annual influenza immunization.

The national and provincial burden of medically attended influenza-associated influenza-like illness and severe acute respiratory illness in the Democratic Republic of Congo, 2013-2015

BACKGROUND

Estimates of influenza-associated outpatient consultations and hospitalizations are severely limited in low- and middle-income countries, especially in Africa.

METHODS

We conducted active prospective surveillance for influenza-like illness (ILI) and severe acute respiratory illness (SARI) at 5 healthcare facilities situated in Kinshasa Province during 2013-2015. We tested upper respiratory tract samples for influenza viruses using a reverse transcription-polymerase chain reaction assay. We estimated age-specific numbers and rates of influenza-associated ILI outpatient consultations and SARI hospitalizations for Kinshasa Province using a combination of administrative and influenza surveillance data. These estimates were extrapolated to each of the remaining 10 provinces accounting for provincial differences in prevalence of risk factors for pneumonia and healthcare-seeking behavior. Rates were reported per 100 000 population.

RESULTS

During 2013-2015, the mean annual national number of influenza-associated ILI outpatient consultations was 1 003 212 (95% Confidence Incidence [CI]: 719 335-1 338 050 - Rate: 1205.3; 95% CI: 864.2-1607.5); 199 839 (95% CI: 153 563-254 759 - Rate: 1464.0; 95% CI: 1125.0-1866.3) among children aged <5 years and 803 374 (95% CI: 567 772-1 083 291 - Rate: 1154.5; 95% CI: 813.1-1556.8) among individuals aged ≥5 years. The mean annual national number of influenza-associated SARI hospitalizations was 40 361 (95% CI: 24 014-60 514 - Rate: 48.5; 95% CI: 28.9-72.7); 25 452 (95% CI: 19 146-32 944 - Rate: 186.5; 95% CI: 140.3-241.3) among children aged <5 years and 14 909 (95% CI: 4868-27 570 - Rate: 21.4; 95% CI: 28.9-72.7) among individuals aged ≥5 years.

CONCLUSIONS

The burden of influenza-associated ILI outpatient consultations and SARI hospitalizations was substantial and was highest among hospitalized children aged <5 years.

Mapping of the US Domestic Influenza Virologic Surveillance Landscape

Influenza virologic surveillance is critical each season for tracking influenza circulation, following trends in antiviral drug resistance, detecting novel influenza infections in humans, and selecting viruses for use in annual seasonal vaccine production. We developed a framework and process map for characterizing the landscape of US influenza virologic surveillance into 5 tiers of influenza testing: outpatient settings (tier 1), inpatient settings and commercial laboratories (tier 2), state public health laboratories (tier 3), National Influenza Reference Center laboratories (tier 4), and Centers for Disease Control and Prevention laboratories (tier 5). During the 2015–16 season, the numbers of influenza tests directly contributing to virologic surveillance were 804,000 in tiers 1 and 2; 78,000 in tier 3; 2,800 in tier 4; and 3,400 in tier 5. With the release of the 2017 US Pandemic Influenza Plan, the proposed framework will support public health officials in modeling, surveillance, and pandemic planning and response.

Attributable Fraction of Influenza Virus Detection to Mild and Severe Respiratory Illnesses in HIV-Infected and HIV-Uninfected Patients, South Africa, 2012-2016

The attributable fraction (AF) of influenza virus detection to illness has not been described for patients in different age groups or with different HIV infection statuses. We compared the age group–specific prevalence of influenza virus infection among patients with influenza-like illness (ILI) or severe acute or chronic respiratory illness (SARI and SCRI, respectively) with that among controls, stratified by HIV serostatus. The overall AF for influenza virus detection to illness was 92.6% for ILI, 87.4% for SARI, and 86.2% for SCRI. Among HIV-uninfected patients, the AF for all syndromes was highest among persons <1 and >65 years of age and lowest among persons 25–44 years of age; this trend was not observed among HIV-infected patients. Overall, influenza viruses when detected in patients with ILI, SARI, or SCRI are likely attributable to illness. This finding is particularly likely among children and the elderly irrespective of HIV serostatus and among HIV-infected persons irrespective of age.

The national burden of influenza-associated severe acute respiratory illness hospitalization in Zambia, 2011-2014

BACKGROUND

Estimates of influenza-associated hospitalization are limited in low- and middle-income countries, especially in Africa.

OBJECTIVE

To estimate the national number of influenza-associated severe acute respiratory illness (SARI) hospitalization in Zambia.

METHODS

We conducted active prospective hospital-based surveillance for SARI at the University Teaching Hospital (UTH) situated in Lusaka Province during 2011-2014. Upper respiratory tract samples were tested for influenza virus using a reverse transcriptase polymerase chain reaction assay. We estimated age-specific rates of influenza-associated SARI hospitalizations for the UTH using census and secondary data on respiratory hospitalizations following estimation approaches recommended by the World Health Organization. We used the UTH hospitalization rates as a proxy for Lusaka Province. These rates were adjusted for each of the remaining 9 provinces based on their prevalence of risk factors for pneumonia and healthcare-seeking behavior. Rates were expressed per 100,000 population.

RESULTS

SARI cases accounted for 77.1% (13 389/17 354) of respiratory admissions at the UTH; 82.7% (11 859/14 344) and 50.8% (1530/3010) among individuals aged <5 and ≥5 years, respectively. Among SARI cases tested, the influenza virus detection rate was 5.5% (152/2734), 4.8% (48/998), and 6.0% (104/1736) among individuals aged <5 and ≥5 years, respectively. The mean annual national number of influenza-associated SARI hospitalizations was 6181 (95% CI: 4321-8041-rate: 43.9; 95% CI: 30.7-57.1); 4669 (95% CI: 3287-6051-rate: 187.7; 95% CI: 132.1-243.3) among children aged <5 years; and 1512 (95% CI: 1037-1987-rate: 13.1; 95% CI: 9.0-17.2) among individuals aged ≥5 years.

CONCLUSIONS

The burden of influenza-associated SARI hospitalizations was substantial and was highest among children aged <5 years.

The national burden of influenza-associated severe acute respiratory illness hospitalization in Rwanda, 2012-2014

Background

Estimates of influenza‐associated hospitalization are severely limited in low‐ and middle‐income countries, especially in Africa.

Objectives

To estimate the national number of influenza‐associated severe acute respiratory illness (SARI) hospitalization in Rwanda.

Methods

We multiplied the influenza virus detection rate from influenza surveillance conducted at 6 sentinel hospitals by the national number of respiratory hospitalization obtained from passive surveillance after adjusting for underreporting and reclassification of any respiratory hospitalizations as SARI during 2012‐2014. The population at risk was obtained from projections of the 2012 census. Bootstrapping was used for the calculation of confidence intervals (CI) to account for the uncertainty associated with all levels of adjustment. Rates were expressed per 100 000 population. A sensitivity analysis using a different estimation approach was also conducted.

Results

SARI cases accounted for 70.6% (9759/13 813) of respiratory admissions at selected hospitals: 77.2% (6783/8786) and 59.2% (2976/5028) among individuals aged <5 and ≥5 years, respectively. Overall, among SARI cases tested, the influenza virus detection rate was 6.3% (190/3022): 5.7% (127/2220) and 7.8% (63/802) among individuals aged <5 and ≥5 years, respectively. The estimated mean annual national number of influenza‐associated SARI hospitalizations was 3663 (95% CI: 2930‐4395—rate: 34.7; 95% CI: 25.4‐47.7): 2637 (95% CI: 2110‐3164—rate: 168.7; 95% CI: 135.0‐202.4) among children aged <5 years and 1026 (95% CI: 821‐1231—rate: 11.3; 95% CI: 9.0‐13.6) among individuals aged ≥5 years. The estimates obtained from both approaches were not statistically different (overlapping CIs).

Conclusions

The burden of influenza‐associated SARI hospitalizations was substantial and was highest among children aged <5 years.

Epidemiology of influenza B/Yamagata and B/Victoria lineages in South Africa, 2005-2014

Background

Studies describing the epidemiology of influenza B lineages in South Africa are lacking.

Methods

We conducted a prospective study to describe the circulation of influenza B/Victoria and B/Yamagata lineages among patients of all ages enrolled in South Africa through three respiratory illness surveillance systems between 2005 and 2014: (i) the Viral Watch (VW) program enrolled outpatients with influenza-like illness (ILI) from private healthcare facilities during 2005–2014; (ii) the influenza-like illnesses program enrolled outpatients in public healthcare clinics (ILI/PHC) during 2012–2014; and (iii) the severe acute respiratory illnesses (SARI) program enrolled inpatients from public hospitals during 2009–2014. Influenza B viruses were detected by virus isolation during 2005 to 2009 and by real-time reverse transcription polymerase chain reaction from 2009–2014. Clinical and epidemiological characteristics of patients hospitalized with SARI and infected with different influenza B lineages were also compared using unconditional logistic regression.

Results

Influenza viruses were detected in 22% (8,706/39,804) of specimens from patients with ILI or SARI during 2005–2014, of which 24% (2,087) were positive for influenza B. Influenza B viruses predominated in all three surveillance systems in 2010. B/Victoria predominated prior to 2011 (except 2008) whereas B/Yamagata predominated thereafter (except 2012). B lineages co-circulated in all seasons, except in 2013 and 2014 for SARI and ILI/PHC surveillance. Among influenza B-positive SARI cases, the detection of influenza B/Yamagata compared to influenza B/Victoria was significantly higher in individuals aged 45–64 years (adjusted odds ratio [aOR]: 4.2; 95% confidence interval [CI]: 1.1–16.5) and ≥65 years (aOR: 12.2; 95% CI: 2.3–64.4) compared to children aged 0–4 years, but was significantly lower in HIV-infected patients (aOR: 0.4; 95% CI: 0.2–0.9).

Conclusion

B lineages co-circulated in most seasons except in 2013 and 2014. Hospitalized SARI cases display differential susceptibility for the two influenza B lineages, with B/Victoria being more prevalent among children and HIV-infected persons.

Label-Free Colorimetric Detection of Influenza Antigen Based on an Antibody-Polydiacetylene Conjugate and Its Coated Polyvinylidene Difluoride Membrane

This study presents an antibody-conjugated polydiacetylene (PDA) and its coated polyvinylidene difluoride (PVDF) membrane. The M149 antibody was hybridized to nano-vesicles consisting of pentacosa-10,12-diynoic acid (PCDA) and dimyristoylphosphatidylcholine (DMPC). After photo-polymerization at 254 nm, the effects on the PDA by antigenic injection were investigated with UV-vis spectroscopy, fluorescence spectroscopy, dynamic light scattering and transmission electron microscopy. Because PDA, an alternating ene-yne molecule, induces a blue-to-red color transition and an interesting fluorescent response by the distortion of its backbone, the biomolecular recognition of an antibody–antigen can be converted into an optical and fluorescent signal. Thus, an influenza antigen was successfully detected with the proposed label-free method. Furthermore, the vesicular system was improved by coating it onto a membrane type sensing platform for its stability and portability. The proposed antibody-PDA composite PVDF membrane has potential for rapid, easy and selective visualization of the influenza virus.

Performance Evaluation of Allplex Respiratory Panels 1, 2, and 3 for Detection of Respiratory Viruses and Influenza A Virus Subtypes

The Allplex respiratory panels 1, 2, and 3 (Allplex) comprise a one-step real-time reverse transcription-PCR assay for the detection of respiratory viruses (RVs) and influenza A subtypes based on multiple detection temperature (MuDT) technology. The performance of the Allplex assay was compared with those of the AdvanSure RV real-time PCR kit (AdvanSure) and the PowerChek pandemic H1N1/H3N2/H5N1 real-time PCR kit (PowerChek) using 417 clinical respiratory specimens. In comparison with the AdvanSure assay for RV detection by each virus, the ranges of positive percent agreement, negative percent agreement, and kappa values with the Allplex assay were 82.8 to 100%, 95.5 to 100%, and 0.85 to 1.00, respectively. For influenza A virus (INF A) subtyping, the kappa values between the Allplex and PowerChek assays were 0.67 and 1.00 for the INF A H1N1-pdm09 and H3 subtypes, respectively. Uniplex PCR and sequencing for samples with discrepant results demonstrated that the majority of results were concordant with those from the Allplex assay. When testing 24 samples, the turnaround and hands-on time required to perform the Allplex assay were 4 h 15 min and 15 min, respectively. In conclusion, the Allplex assay produced results comparable to those from the AdvanSure and PowerChek assays.

Cost-effectiveness of seasonal inactivated influenza vaccination among pregnant women

OBJECTIVE

To evaluate the cost-effectiveness of seasonal inactivated influenza vaccination among pregnant women using data from three recent influenza seasons in the United States.

DESIGN, SETTING, AND PARTICIPANTS

We developed a decision-analytic model following a cohort of 5.2 million pregnant women and their infants aged <6 months to evaluate the cost-effectiveness of vaccinating women against seasonal influenza during pregnancy from a societal perspective. The main outcome measures were quality-adjusted life-year (QALY) gained and cost-effectiveness ratios. Data sources included surveillance data, epidemiological studies, and published vaccine cost data. Sensitivity analyses were also performed. All costs and outcomes were discounted at 3% annually.

MAIN OUTCOME MEASURES

Total costs (direct and indirect), effects (QALY gains, averted case numbers), and incremental cost-effectiveness of seasonal inactivated influenza vaccination among pregnant women (cost per QALY gained).

RESULTS

Using a recent benchmark of 52.2% vaccination coverage among pregnant women, we studied a hypothetical cohort of 2,753,015 vaccinated pregnant women. With an estimated vaccine effectiveness of 73% among pregnant women and 63% among infants <6 months, QALY gains for each season were 305 (2010-2011), 123 (2011-2012), and 610 (2012-2013). Compared with no vaccination, seasonal influenza vaccination during pregnancy was cost-saving when using data from the 2010-2011 and 2012-2013 influenza seasons. The cost-effectiveness ratio was greater than $100,000/QALY with the 2011-2012 influenza season data, when CDC reported a low attack rate compared to other recent seasons.

CONCLUSIONS

Influenza vaccination for pregnant women can reduce morbidity from influenza in both pregnant women and their infants aged <6 months. Seasonal influenza vaccination during pregnancy is cost-saving during moderate to severe influenza seasons.

Improving Accuracy of Influenza-Associated Hospitalization Rate Estimates

Adjusting for diagnostic test sensitivity enables more accurate and timely comparisons over time.

Diagnostic test sensitivity affects rate estimates for laboratory-confirmed influenza–associated hospitalizations. We used data from FluSurv-NET, a national population-based surveillance system for laboratory-confirmed influenza hospitalizations, to capture diagnostic test type by patient age and influenza season. We calculated observed rates by age group and adjusted rates by test sensitivity. Test sensitivity was lowest in adults >65 years of age. For all ages, reverse transcription PCR was the most sensitive test, and use increased from <10% during 2003–2008 to ≈70% during 2009–2013. Observed hospitalization rates per 100,000 persons varied by season: 7.3–50.5 for children <18 years of age, 3.0–30.3 for adults 18–64 years, and 13.6–181.8 for adults >65 years. After 2009, hospitalization rates adjusted by test sensitivity were ≈15% higher for children <18 years, ≈20% higher for adults 18–64 years, and ≈55% for adults >65 years of age. Test sensitivity adjustments improve the accuracy of hospitalization rate estimates.

Surveillance for severe acute respiratory infections in Southern Arizona, 2010-2014

Background

The Binational Border Infectious Disease Surveillance program began surveillance for severe acute respiratory infections (SARI) on the US–Mexico border in 2009. Here, we describe patients in Southern Arizona.

Methods

Patients admitted to five acute care hospitals that met the SARI case definition (temperature ≥37·8°C or reported fever or chills with history of cough, sore throat, or shortness of breath in a hospitalized person) were enrolled. Staff completed a standard form and collected a nasopharyngeal swab which was tested for selected respiratory viruses by reverse transcription polymerase chain reaction.

Results

From October 2010–September 2014, we enrolled 332 SARI patients. Fifty‐two percent were male and 48% were white non‐Hispanic. The median age was 63 years (47% ≥65 years and 5·2% <5 years). During hospitalization, 51 of 230 (22%) patients required intubation, 120 of 297 (40%) were admitted to intensive care unit, and 28 of 278 (10%) died. Influenza vaccination was 56%. Of 309 cases tested, 49 (16%) were positive for influenza viruses, 25 (8·1%) for human metapneumovirus, 20 (6·5%) for parainfluenza viruses, 16 (5·2%) for coronavirus, 11 (3·6%) for respiratory syncytial virus, 10 (3·2%) for rhinovirus, 4 (1·3%) for rhinovirus/enterovirus, 3 (1·0%) for enteroviruses, and 3 (1·0%) for adenovirus. Among the 49 influenza‐positive specimens, 76% were influenza A (19 H3N2, 17 H1N1pdm09, and 1 not subtyped), and 24% were influenza B.

Conclusion

Influenza viruses were a frequent cause of SARI in hospitalized patients in Southern Arizona. Monitoring respiratory illness in border populations will help better understand the etiologies. Improving influenza vaccination coverage may help prevent some SARI cases.

Survey of influenza and other respiratory viruses diagnostic testing in US hospitals, 2012-2013

Background

Little is known about laboratory capacity to routinely diagnose influenza and other respiratory viruses at clinical laboratories and hospitals.

Aims

We sought to assess diagnostic practices for influenza and other respiratory virus in a survey of hospitals and laboratories participating in the US Influenza Hospitalization Surveillance Network in 2012–2013.

Materials and Methods

All hospitals and their associated laboratories participating in the Influenza Hospitalization Surveillance Network (FluSurv‐NET) were included in this evaluation. The network covers more than 80 counties in 15 states, CA, CO, CT, GA, MD, MN, NM, NY, OR, TN, IA, MI, OH, RI, and UT, with a catchment population of ~28 million people. We administered a standardized questionnaire to key personnel, including infection control practitioners and laboratory departments, at each hospital through telephone interviews.

Results

Of the 240 participating laboratories, 67% relied only on commercially available rapid influenza diagnostic tests to diagnose influenza. Few reported the availability of molecular diagnostic assays for detection of influenza (26%) and other viral pathogens (≤20%) in hospitals and commercial laboratories.

Conclusion

Reliance on insensitive assays to detect influenza may detract from optimal clinical management of influenza infections in hospitals.

Influenza in the Emergency Department: Vaccination, Diagnosis, and Treatment: Clinical Practice Paper Approved by American Academy of Emergency Medicine Clinical Guidelines Committee

BACKGROUND

Influenza is an acute respiratory virus that results in significant worldwide morbidity and mortality each year. As emergency physicians, we are often the first to encounter patients with seasonal influenza. It is therefore critical that we draw on the most recent and relevant research when we make clinical decisions regarding the diagnosis, treatment, and prophylaxis of this disease.

METHODS

A MEDLINE literature search from August 2009 to August 2015 was performed using the keywords influenza vaccination efficacy AND systematic, influenza AND rapid antigen testing, and Oseltamivir AND systematic, while limiting the search to human studies written in the English language. General review articles and case reports were omitted. Each of the selected articles then underwent a structured review.

RESULTS

We identified 163 articles through our literature search, of which 68 were found to be relevant to our clinical questions. These studies then underwent a rigorous review from which recommendations were given.

CONCLUSIONS

Influenza vaccine efficacy continues to range between 40% and 80%. Vaccination has the potential to decrease disease severity and is recommended for individuals older than 6 months of age. If resources permit, vaccination can be offered to patients presenting to the emergency department. Rapid antigen detection for influenza is a simple bedside test with high specificity, but generally low sensitivity. If a patient presents with a syndrome consistent with influenza and has negative rapid antigen detection, they should either receive a confirmatory reverse transcriptase polymerase chain reaction or be treated as if they have influenza. Treatment with neuraminidase inhibitors can decrease the duration of influenza and is recommended in hospitalized patients, or in those with high risk of complications.

Colorimetric detection of influenza A (H1N1) virus by a peptide-functionalized polydiacetylene (PEP-PDA) nanosensor

​We developed a peptide-functionalized polydiacetylene nanosensor for pH1N1 virus detection with the naked eye.

Comparison of the AdvanSure™ real-time RT-PCR and Seeplex(®) RV12 ACE assay for the detection of respiratory viruses

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Analytical performance was examined using consecutive clinical specimens.

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The AdvanSure assay required less hands-on and turnaround times than the Seeplex assay.

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The results of respiratory viruses detection were comparable in both assays.

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The AdvanSure assay showed a higher concordance with monoplex PCR and sequencing.

The AdvanSure™ RV real-time PCR kit (AdvanSure; LG Life Sciences, Korea) is based on multiplex real-time PCR and can simultaneously detect 14 respiratory viruses. We compared the performance of the AdvanSure assay with the Seeplex RV 12 ACE detection kit (Seeplex; Seegene, Seoul, South Korea), a multiplex end-point PCR assay. A total of 454 consecutive respiratory specimens were tested with both AdvanSure and Seeplex assays; AdvanSure detected 153 (33.7%) positive cases and Seeplex detected 145 (31.9%) positive cases. The positive percent agreement, negative percent agreement, and kappa value for the two assays were 87.2% (95% CI, 80.3–92.1), 91.1% (95% CI, 87.2–93.9), and 0.77 (95% CI, 0.70–0.83), respectively. Compared with the Seeplex assay, the AdvanSure assay had a shorter turnaround time (3 h vs. 8 h) and a shorter hands-on time (<1 h vs 2 h). In conclusion, the AdvanSure assay demonstrated comparable performance to the Seeplex assay.

Effect of rapid influenza diagnostic testing on antiviral treatment decisions for patients with influenza-like illness: southwestern U.S., May-December 2009

Rapid influenza diagnostic tests (RIDTs) had low test sensitivity for detecting 2009 pandemic influenza A (H1N1pdm09) infection, causing public health authorities to recommend that treatment decisions be based primarily upon risk for influenza complications. We used multivariate Poisson regression analysis to estimate the contribution of RIDT results and risk for H1N1pdm09 complications to receipt of early antiviral (AV) treatment among 290 people with influenza-like illness (ILI) who received an RIDT ≤48 hours after symptom onset from May to December 2009 at four southwestern U.S. facilities. RIDT results had a stronger association with receipt of early AVs (rate ratio [RR] = 3.3, 95% confidence interval [CI] 2.4, 4.6) than did the presence of risk factors for H1N1pdm09 complications (age <5 years or high-risk medical conditions) (RR=1.9, 95% CI 1.3, 2.7). Few at-risk people (28/126, 22%) who had a negative RIDT received early AVs, suggesting the need for sustained efforts by public health to influence clinician practices.

Speed versus coverage trade off in targeted interventions during an outbreak

Which case-based intervention measures should be applied during an epidemic outbreak depends on how timely they can be applied and how effective they are. During the course of each individual's infection, the earlier control measures are applied on him/her the more effectively further disease spread can be prevented. However, quick implementation can lead to loss of efficacy or coverage, e.g., when individuals are targeted based on rapid but poorly sensitive diagnostic tests in place of slower but accurate PCR tests. To analyse this trade off between speed and coverage we used stochastic models considering how the individual reproduction density is modified by interventions. We took as example the case-based intervention strategy employed in the Netherlands during the beginning of the H1N1 pandemic. Suspected cases were isolated and samples were collected for PCR diagnosis. In case of positive diagnosis, antiviral drugs were provided to contacts as post-exposure prophylaxis. At the time there were also rapid influenza diagnostic tests (RIDTs) available which provided results within an hour after sample collection compared to a median of 2.7 days for PCR tests, but they were less sensitive. We studied how interventions based on RIDTs with various sensitivities affect the outbreak size and how these compare to PCR diagnosis based interventions. Using an intervention based on a bedside RIDT with 60% detection ratio or a laboratory RIDT with 70% detection ratio is as effective as the most effective PCR-diagnosis based intervention. Relative performances of interventions are not dependent on the basic reproduction number R0 but only on distributions of individual reproduction density and of delay periods. The individual reproduction density combines R0 and infection time distribution, both crucial in determining the impact of case-based interventions during epidemic outbreaks.

A prospective study of Romanian agriculture workers for zoonotic influenza infections

Background

In this prospective study we sought to examine seroepidemiological evidence for acute zoonotic influenza virus infection among Romanian agricultural workers.

Methods

Sera were drawn upon enrollment (2009) and again at 12 and 24 months from 312 adult agriculture workers and 51 age-group matched controls. Participants were contacted monthly for 24 months and queried regarding episodes of acute influenza-like illnesses (ILI). Cohort members meeting ILI criteria permitted respiratory swab collections as well as acute and convalescent serum collection. Serologic assays were performed against 9 avian, 3 swine, and 3 human influenza viruses.

Results

During the two-year follow-up, a total of 23 ILI events were reported. Two subjects' specimens were identified as influenza A by rRT-PCR. During the follow-up period, three individuals experienced elevated microneutralization antibody titers ≥1∶80 against three (one each) avian influenza viruses: A/Teal/Hong Kong/w312/97(H6N1), A/Hong Kong/1073/1999(H9N2), or A/Duck/Alberta/60/1976(H12N5). However, none of these participants met the criteria for poultry exposure. A number of subjects demonstrated four-fold increases over time in hemagglutination inhibition (HI) assay titers for at least one of the three swine influenza viruses (SIVs); however, it seems likely that two of these three responses were due to cross-reacting antibody against human influenza. Only elevated antibody titers against A/Swine/Flanders/1/1998(H3N2) lacked evidence for such confounding. In examining risk factors for elevated antibody against this SIV with multiple logistic regression, swine exposure (adjusted OR = 1.8, 95% CI 1.1–2.8) and tobacco use (adjusted OR = 1.8; 95% CI 1.1–2.9) were important predictors.

Conclusions

While Romania has recently experienced multiple incursions of highly pathogenic avian influenza among domestic poultry, this cohort of Romanian agriculture workers had sparse evidence of avian influenza virus infections. In contrast, there was evidence, especially among the swine exposed participants, of infections with human and one swine H3N2 influenza virus.

Little evidence of subclinical avian influenza virus infections among rural villagers in Cambodia

In 2008, 800 adults living within rural Kampong Cham Province, Cambodia were enrolled in a prospective cohort study of zoonotic influenza transmission. After enrollment, participants were contacted weekly for 24 months to identify acute influenza-like illnesses (ILI). Follow-up sera were collected at 12 and 24 months. A transmission substudy was also conducted among the family contacts of cohort members reporting ILI who were influenza A positive. Samples were assessed using serological or molecular techniques looking for evidence of infection with human and avian influenza viruses. Over 24 months, 438 ILI investigations among 284 cohort members were conducted. One cohort member was hospitalized with a H5N1 highly pathogenic avian influenza (HPAI) virus infection and withdrew from the study. Ninety-seven ILI cases (22.1%) were identified as influenza A virus infections by real-time RT-PCR; none yielded evidence for AIV. During the 2 years of follow-up, 21 participants (3.0%) had detectable antibody titers (≥1∶10) against the studied AIVs: 1 against an avian-like A/Migratory duck/Hong Kong/MPS180/2003(H4N6), 3 against an avian-like A/Teal/Hong Kong/w312/97(H6N1), 9 (3 of which had detectible antibody titers at both 12- and 24-month follow-up) against an avian-like A/Hong Kong/1073/1999(H9N2), 6 (1 detected at both 12- and 24-month follow-up) against an avian-like A/Duck/Memphis/546/74(H11N9), and 2 against an avian-like A/Duck/Alberta/60/76(H12N5). With the exception of the one hospitalized cohort member with H5N1 infection, no other symptomatic avian influenza infections were detected among the cohort. Serological evidence for subclinical infections was sparse with only one subject showing a 4-fold rise in microneutralization titer over time against AvH12N5. In summary, despite conducting this closely monitored cohort study in a region enzootic for H5N1 HPAI, we were unable to detect subclinical avian influenza infections, suggesting either that these infections are rare or that our assays are insensitive at detecting them.

Preparing ICUs for pandemics

PURPOSE OF REVIEW

Influenza pandemics occur intermittently and represent an existential global infectious diseases threat. The purpose of this review is to describe clinical and research preparedness for future pandemics.

RECENT FINDINGS

Pandemic influenza typically results in large numbers of individuals with life-threatening pneumonia requiring treatment in ICUs. Clinical preparedness of ICUs relates to planning to provide increased 'surge' capacity to meet increased demand and requires consideration of staffing, equipment and consumables, bed-space availability and management systems. Research preparedness is also necessary, as timely clinical research has the potential to change the trajectory of a pandemic. The clinical research response during the 2009 H1N1 influenza pandemic was suboptimal.

SUMMARY

Better planning is necessary to optimize both clinical and research responses to future pandemics.

Evidence for subclinical H5N1 avian influenza infections among Nigerian poultry workers

In recent years Nigeria has experienced sporadic incursions of highly pathogenic H5N1 avian influenza among poultry. In 2008, 316 poultry-exposed agricultural workers, and 54 age-group matched non-poultry exposed adults living in the Enugu or Ebonyi States of Nigeria were enrolled and then contacted monthly for 24 months to identify acute influenza-like-illnesses. Annual follow-up sera and questionnaire data were collected at 12 and 24 months. Participants reporting influenza-like illness completed additional questionnaires, and provided nasal and pharyngeal swabs and acute and convalescent sera. Swab and sera specimens were studied for evidence of influenza A virus infection. Sera were examined for elevated antibodies against 12 avian influenza viruses by microneutralization and 3 human viruses by hemagglutination inhibition. Four (3.2%) of the 124 acute influenza-like-illness investigations yielded molecular evidence of influenza, but virus could not be cultured. Serial serum samples from five poultry-exposed subjects had a ≥4-fold change in microneutralization titers against A/CK/Nigeria/07/1132123(H5N1), with three of those having titers ≥1:80 (maximum 1:1,280). Three of the five subjects (60%) reported a preceding influenza-like illness. Hemagglutination inhibition titers were ≥4-fold increases against one of the human viruses in 260 participants. While cross-reactivity from antibodies against other influenza viruses cannot be ruled out as a partial confounder, over the course of the 2-year follow-up, at least 3 of 316 (0.9%) poultry-exposed subjects had evidence for subclinical HPAI H5N1 infections. If these data represent true infections, it seems imperative to increase monitoring for avian influenza among Nigeria's poultry and poultry workers.

Comparison of the Anyplex(TM) II RV16 and Seeplex(®) RV12 ACE assays for the detection of respiratory viruses

The Anyplex^TM II RV16 detection kit (RV16; Seegene, Seoul, South Korea) is a multiplex real-time PCR assay based on tagging oligonucleotide cleavage extension. In this prospective study, we evaluated the RV16 assay by comparing with the Seeplex^® RV12 ACE detection kit (RV12; Seegene), a multiplex end-point PCR kit. A total of 365 consecutive respiratory specimens were tested with both RV16 and RV12 assays in parallel and detected 140 (38.4%) and 89 (24.4%) positive cases, respectively. The positive percent agreement, negative percent agreement, and kappa values for the 2 assays were 95.6% (95% confidence interval [CI], 89.4–98.3%), 80.4% (95% CI, 75.3–84.6%), and 0.64 (95% CI, 0.56–0.72), respectively. The monoplex PCR and sequencing for the samples with discrepant results revealed that majority of the results were concordant with the results from RV16 assays. In conclusion, the RV16 assay produces results comparable to the RV12 assay.

Little evidence of avian or equine influenza virus infection among a cohort of Mongolian adults with animal exposures, 2010-2011

Avian (AIV) and equine influenza virus (EIV) have been repeatedly shown to circulate among Mongolia’s migrating birds or domestic horses. In 2009, 439 Mongolian adults, many with occupational exposure to animals, were enrolled in a prospective cohort study of zoonotic influenza transmission. Sera were drawn upon enrollment and again at 12 and 24 months. Participants were contacted monthly for 24 months and queried regarding episodes of acute influenza-like illnesses (ILI). Cohort members confirmed to have acute influenza A infections, permitted respiratory swab collections which were studied with rRT-PCR for influenza A. Serologic assays were performed against equine, avian, and human influenza viruses. Over the 2 yrs of follow-up, 100 ILI investigations in the cohort were conducted. Thirty-six ILI cases (36%) were identified as influenza A infections by rRT-PCR; none yielded evidence for AIV or EIV. Serological examination of 12 mo and 24 mo annual sera revealed 37 participants had detectable antibody titers (≥1∶10) against studied viruses during the course of study follow-up: 21 against A/Equine/Mongolia/01/2008(H3N8); 4 against an avian A/Teal/Hong Kong/w3129(H6N1), 11 against an avian-like A/Hong Kong/1073/1999(H9N2), and 1 against an avian A/Migrating duck/Hong Kong/MPD268/2007(H10N4) virus. However, all such titers were <1∶80 and none were statistically associated with avian or horse exposures. A number of subjects had evidence of seroconversion to zoonotic viruses, but the 4-fold titer changes were again not associated with avian or horse exposures. As elevated antibodies against seasonal influenza viruses were high during the study period, it seems likely that cross-reacting antibodies against seasonal human influenza viruses were a cause of the low-level seroreactivity against AIV or EIV. Despite the presence of AIV and EIV circulating among wild birds and horses in Mongolia, there was little evidence of AIV or EIV infection in this prospective study of Mongolians with animal exposures.

Pandemic preparedness and the Influenza Risk Assessment Tool (IRAT)

Influenza infections have resulted in millions of deaths and untold millions of illnesses throughout history. Influenza vaccines are the cornerstone of influenza prevention and control. Recommendations are made by the World Health Organization (WHO) 6-9 months in advance of the influenza season regarding what changes, if any, should be made in the formulation of seasonal influenza vaccines. This allows time to manufacture, test, distribute, and administer vaccine prior to the beginning of the influenza season. At the same time experts also consider which viruses not currently circulating in the human population, but with pandemic potential, pose the greatest risk to public health. Experts may conclude that one or more of these viruses are of enough concern to warrant development of a high-growth reassortant candidate vaccine virus. Subsequently, national authorities may determine that a vaccine should be manufactured, tested in clinical trials, and even stockpiled in some circumstances. The Influenza Risk Assessment Tool (IRAT) was created in an effort to develop a standardized set of elements that could be applied for decision making when evaluating pre-pandemic viruses. The tool is a simple, additive model, based on multi-attribute decision analysis . The ultimate goal is to identify an appropriate candidate vaccine virus and prepare a human vaccine before the virus adapts to infect and efficiently transmit in susceptible human populations. This pre-pandemic preparation allows production of vaccine-a strategy that could save lives and mitigate illness during a pandemic.