Infectious Diseases

Influenza Viruses

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OVERVIEW: What every clinician needs to know

Pathogen name and classification

Influenza viruses (types A, B, C) are segmented, negative-strand ribonucleic acid (RNA) viruses in the Orthomyxoviridae family. Influenza A viruses of various subtypes infect many animal species (e.g., birds, swine, horses, dogs, marine mammals, and felids) in addition to humans. Influenza A viruses are classified into subtypes by their surface glycoproteins with 17 hemagglutinin (HA) and 10 neuraminidase (NA) subtypes currently recognized. Wild aquatic birds are the primary reservoir for these many subtypes, but certain HA subtypes have adapted to and circulated widely in mammalian hosts (e.g., H1-3 in humans, H1 and H3 in swine, H3 and H7 in horses, and H3 in dogs) or domestic poultry (e.g., H5, H7 and H9). One subtype H17N10 has been detected in bats. Influenza B and C viruses are primarily human pathogens. Influenza viruses are designated by their host source (i.e., human, other animal), type, location/sample, number/year of isolation, and subtype for influenza A viruses (e.g., A/Perth/16/2009[H3N2]).

What is the best treatment?

Neuraminidase inhibitors—oseltamivir, zanamivir

  • Oral oseltamivir and orally inhaled zanamivir, which requires use of a specific device (Diskhaler®), are inhibitory for almost all currently circulating strains of influenza A and B viruses. Prospective randomized controlled trials (RCTs) show that their early therapeutic use (<2 days after illness onset) in ambulatory patients with febrile influenza illness reduces the duration of illness, time to resume usual activities, and the risk of physician-diagnosed respiratory complications leading to antibiotic use. This includes the risk of new otitis media diagnoses in young children and, acute bronchitis in adults.

  • Observational studies indicate that oseltamivir treatment reduces the likelihood of pneumonia, hospitalization and mortality, and the duration of hospitalization in those hospitalized with seasonal or pandemic 2009 H1N1 (A(H1N1)pdm09) virus infection. Mortality reduction in those hospitalized, even when treatment has been initiated as late as 5 days after illness onset. Treatment appears to reduce the likelihood of progression to pneumonia and death in risk groups like pregnant women, and in severely immunocompromised hosts, including hematopoietic stem cell (HSCT) and solid organ transplant recipients. However, progressive illness and mortality due to inadequately controlled viral replication, bacterial suprainfection, deteiroration in underlying conditions, or other complications may occur despite early antiviral treatment.

  • A mortality benefit has been reported in avian A(H5N1)-infected patients treated up to about 1 week after illness onset, but mortality is very high in those treated after onset of respiratory failure.

General recommendations for use

  • Antiviral treatment is indicated as soon as possible after illness onset, for patients with suspected or proven influenza who have severe, complicated, or progressive illness; those who require hospitalization; for outpatients with suspected or confirmed influenza who are at higher risk of influenza complications because of age or underlying medical conditions: and in suspected or proven infections due to virulent viruses like avian A(H5N1) or A(H7N9).

  • Clinical judgment is an essential part of treatment decisions, particularly in outpatients.

  • Neuraminidase inhibitor (NAI) therapy may be considered for any previously healthy outpatient with febrile influenza who presents for care within 2 days of illness onset.

  • Treatment should not be delayed while waiting for laboratory confirmation and should be undertaken empirically, particularly in hospitalized or seriously ill patients, despite presentation beyond 48 hours after illness onset.

Dosing regimens

  • The standard dose regimens (Table I) are based largely on studies in uncomplicated illness, and the optimal dosages and duration of therapy are inadequately studied in seriously ill or immunocompromised patients.

Table I

  • Although a standard 5-day oseltamivir regimen appears adequate for most outpatients and hospitalized patients with infection due to susceptible strains, the more prolonged duration of viral replication in those with viral or mixed viral-bacterial pneumonias and case reports of clinical deterioration after cessation of a 5-day regimen indicates likely need for more protracted therapy in those with serious or progressive illness, immunocompromised status, or in serious zoonotic infections with viruses like avian A(H5N1) or A(H7N9) (e.g., 10 days).

  • A double-dose regimen of oseltamivir (i.e., 150mg twice daily in adults) has adequate tolerability but has not been shown to be superior to standard doses in RCTs of ambulatory or hospitalized patients with seasonal influenza, although it has not been adequately studied in those with severe viral pneumonia.

  • Oseltamivir is less active against influenza B compared with influenza A NAs in vitro and has been associated with slower clinical and virologic responses in influenza B-infected children compared with influenza A-infected children.

  • A double-dose oseltamivir regimen is a reasonable consideration in influenza B virus infections in immunocompromised hosts, in serious illness due to influenza B virus or zoonotic viruses like avian A(H5N1) or A(H7N9), and in those with severe or progressive viral pneumonia. Zanamivir is an effective agent for treatment of uncomplicated influenza and is the current agent of choice when oseltamivir resistance is suspected. Limited data suggest that inhaled zanamivir may be superior to oseltamivir in treating uncomplicated influenza B infections.

    • Orally inhaled zanamivir has received very little study in patients with serious or progressive illness, and concerns exist about possible bronchospasm and inadequate delivery to sites of viral infection in the lower respiratory tract, particularly when pneumonia is present.

    • Inhaled zanamivir is generally not recommended for treating influenza patients with underlying airways disease like asthma and COPD because of the risk of provoking bronchospasm.

    • Nebulized delivery of an investigational aqueous formulation has been used in some immunocompromised or severely ill patients, including those receiving mechanical ventilation. However, the commercial powder formulation, which contains a lactose carrier, should not be used under such circumstances as it has been associated with blocking of ventilator filters and fatal outcome in at least one patient.

    • Intravenous zanamivir would be the agent of choice for treating serious infections due to oseltamivir-resistant virus. Intravenous zanamivir is currently available on a compassionate use basis from its manufacturer.

Specific risk groups

  • Renal insufficiency, dialysis. Both NAIs are cleared primarily through urinary excretion. Inhaled zanamivir has low systemic exposure and does not require dose adjustment in such patients. In contrast, oseltamivir dose adjustments are required for creatinine clearance less than 30mL/min, and increasing degrees of renal insufficiency and specific types of renal replacement therapy require further adjustments (consult the US Centers for Disease Control and Prevention [CDC] guidelines or manufacturer recommendations).

  • Neonates, prematures, and young infants. Oseltamivir is now approved for use in infants 2 weeks of age and older, and has been used during both seasonal and A(H1N1)pdm09 influenza in very young infants for both prophylaxis (neonatal unit outbreaks) and therapy with apparent acceptable tolerability. Of note, the pharmacology of oseltamivir changes substantially during maturation in infants, and dosing adjustments are required for both age and weight (consult the CDC or the World Health Organization [WHO] recommendations).

  • Pregnant and early postpartum women. NAIs are classified as Pregnancy Category C agents, although preclinical studies and pregnancy registries of exposed women have not found evidence for teratogenic risks to date, nor has the frequency of adverse maternal or fetal outcomes been elevated above background rates. Early NAI treatment was associated with improved outcomes, including reduced intensive care unit (ICU) admissions and death during the 2009 pandemic.

    • Inconsistent results have been found in studies to date with regard to changes in oseltamivir pharmacokinetics during pregnancy, but reduced blood levels of the active metabolite, oseltamivir carboxylate, may occur in later stages of pregnancy. Consequently, until further data are available, double-dose therapy (150mg twice daily) would be reasonable for any pregnant or early postpartum woman with severe or progressive influenza illness.

  • Obesity. No important differences in oseltamivir pharmacokinetics have been found in several studies of obese or morbidly obese persons, but more data are needed in those with morbid obesity to assess the possible need for dosage increase.

  • Cystic fibrosis. The exposure to oseltamivir carboxylate, based on plasma area-under-the-curve over time, is reduced by about 30% compared to healthy persons, and higher doses (e.g., 100mg twice daily) have been suggested. Given the tolerability of oseltamivir, double-dose (150mg twice daily in adults) therapy would be reasonable for older cystic fibrosis patients, particularly those with severe or progressive influenza illness.

  • Immunocompromised hosts. Given the challenges in diagnosis and goal of avoiding subtherapeutic drug levels, twice daily dosing is advised for postexposure prophylaxis, instead of standard once daily prophylactic dosing. For treatment of established illness, it remains to be determined whether higher than standard oseltamivir doses provide greater therapeutic benefit or reduces risk of resistance emergence. However, double-dose oseltamivir would be reasonable in immunocompromised hosts with serious illness or influenza B virus infections. Immunocompromised patients frequently have detectable viral replication beyond 5 days treatment, so that prolonged courses and monitoring for resistance emergence may be required.

Antiviral resistance

  • Resistance to NAIs, particularly to oseltamivir, may emerge during therapy, in those failing chemoprophylaxis, and sometimes de novo in circulating strains. The frequency of resistance emergence during therapy depends on virus NA type and subtype, patient age, and the NAI used.

  • Resistance to NAIs arises most commonly from single amino acid mutations in viral NA that impair NAI binding to the active enzyme site. The responsible mutations, the magnitude of resistance or reduced susceptibility, and the fitness costs (effects on replication or transmission) for the virus vary by NA type and subtype and drug. The most commonly recognized mutations conferring oseltamivir resistance are His275Tyr in N1 and Arg292Lys and Glu119Val in N2 NAs, although an increasing variety of mutations causing reduced susceptibility to NAIs are being recognized.

  • When oseltamivir has been used for treatment of seasonal influenza, resistance has been found to emerge in approximately 1% of outpatient adults and 4 to 27% of outpatient and inpatient children and is generally more common in N1 than N2-containing viruses, including up to 25% of avian A(H5N1)-infected persons.

  • Oseltamivir resistance generally emerges after 4 or more days of therapy but sometimes as early as 2 days after starting administration. Development of oseltamivir resistance is more frequent in severely immuncompromised hosts who may manifest prolonged viral replication lasting weeks to months. Immuncompromised hosts hospitalized with A(H1N1)pdm09 illness experienced emergence of oseltamivir resistance frequently, often associated with serious consequences, including death and, in several instances, with nosocomial transmission of resistant variants.

  • Resistance to zanamivir appears to be very uncommon, although viruses with reduced susceptibility to zanamivir and other NAIs (e.g., IIe223Arg in N1, Arg152LYs in B) have emerged in highly immunocompromised hosts and have been reported in influenza B viruses in the community (e.g., Asp198Asn, IIe222Thr).

  • Resistance to NAIs arises most commonly from single amino acid mutations in viral NA that impair NAI binding to the active enzyme site. The responsible mutations, the magnitude of resistance or reduced susceptibility, and the fitness costs (effects on replication or transmission) for the virus vary by NA type and subtype and drug. The most commonly recognized mutations conferring oseltamivir resistance are His275Tyr in N1 and Arg292Lys and Glu119Val in N2 NAs, although an increasing variety of mutations causing reduced susceptibility to NAIs are being recognized.

  • Seasonal A(H1N1) resistance. The H257Y mutation in the N1 NA causes marked loss of in vitro susceptibility (generally >300-fold) and of clinical effectiveness. Global circulation of oseltamivir-resistant seasonal A(H1N1) virus harboring a H275Y mutation was not related to oseltamivir usage, and, of note, the oseltamivir-resistant A/Brisbane/59/07(H1N1) virus replaced the oseltamivir-susceptible parental one, an indication that the resistant virus possessed greater transmission fitness. This was perhaps because of better functional balance between virus HA-mediated attachment to cellular receptors and NA receptor-destroying activity, with enabling mutations in viral NA, perhaps mutations in other genes that enhanced replication, or slight differences in HA antigenicity.

  • Pandemic A(H1N1) resistance. The H275Y mutation has been found in approximately 1 to 2% of A(H1N1)pdm09 isolates tested to date. Although this oseltamivir-resistance mutation has been found primarily in those given oseltamivir for treatment or prophylaxis, particularly in immunocompromised hosts, an increasing proportion of resistant variants have been found recently in community isolates from persons with no known drug exposure. Community clusters of oseltamivir-resistant A(H1N1)pdm09 viruses have been reported from Australia and Vietnam, so vigilance is essential in monitoring susceptibility patterns.

  • Drug susceptibility testing. Both genotypic (e.g., direct NA gene sequencing, mutation-specific nucleic acid amplification tests (NATs)) and phenotypic (e.g., NA enzyme inhibition assays) are available for detecting specific resistance mutations and alterations in in vitro susceptibility, respectively. Genotypic assays are generally much more rapid, but, because they are targeted to detecting one or more recognized mutations, they miss others and novel ones. Phenotypic assays are needed to detect and assess the possible significance of novel mutations but are more time-consuming and technically demanding. Comprehensive susceptibility testing is available through the CDC and some state and academic laboratories; mutation-specific testing is available through a wider range of hospital and state laboratories, as well as several commercial ones.

    • Population groups at higher risk of resistance emergence during NAI therapy include young children, immunocompromised hosts (particularly those with hematologic malignancies or HSCT), and patients with persisting viral detection in the setting of severe or progressive illness.

    • The primary reason to obtain susceptibility testing in an individual patient is to determine whether to change antiviral therapy or to confirm that a prior empiric switch was correct in retrospect.

    • In immunocompromised patients and seriously ill hospitalized patients, serial virologic monitoring to document viral clearance can provide evidence for virologic failure and need for susceptibility testing.

    • Standard definitions for virologic failure are not agreed at present, but recovery of infectious virus or persisting high levels of viral RNA (low cycle threshold [Ct] values) after 5 days of antiviral therapy should raise concern. Epidemiologic clues include patients failing antiviral prophylaxis in an institutional outbreak setting or those developing illness after exposure to treated ill persons, particularly if immunocompromised.

    • Most, but not all (e.g., Arg292Lys in N2, IIe223Arg in N1, Asp198Asn in B), oseltamivir-resistant variants retain susceptibility to zanamivir and the investigational inhaled NAI laninamivir. Zanamivir is the current agent of choice for treating such infections, and its intravenous formulation (currently investigational but available on compassionate use basis) would be preferred for use in those with serious illness. The oseltamivir-resistant seasonal A/Brisbane/59/07(H1N1) was susceptible to adamantanes, but recently circulating influenza A viruses (A(H3N2), A(H1N1)pdm09) have been almost uniformly resistant to this antiviral class. Several investigational agents with novel mechanisms of action are inhibitory for viruses resistant to NAIs and adamantanes.

Investigational neuraminidase inhibitors—intravenous, inhaled

Intravenous neuraminidase inhibitors

  • Intravenous (IV) administration of NAIs can provide rapid, reliable delivery of therapeutic drug levels in seriously ill patients, and intravenous zanamivir or peramivir provides peak plasma concentrations approximately 50-fold or higher than those observed with oral oseltamivir. Although oseltamivir, when administered extemporaneously via nasogastric tube in critically ill patients, appears to be absorbed in most patients, concerns remain that gastric stasis or other factors might reduce absorption in some patients.

  • IV zanamivir (GlaxoSmithKline, 600mg every 12 hours in adults) was used on a compassionate-use basis in many severely ill A(H1N1)pdm09 patients, particularly those with suspected or proven oseltamivir resistance, and appeared to be associated with substantial antiviral effects and acceptable tolerance. It is undergoing phase 3 studies in hospitalized patients at present but is also available on compassionate use basis (available using an emergency investigational new drug [eIND] application in the United States) from its manufacturer (GlaxoSmithKline). IV zanamivir is currently the drug of choice for seriously ill patients with infections due to suspected or proven oseltamivir resistant viruses.

  • IV peramivir (Biocryst) was used widely in severely ill A(H1N1)pdm09 patients in the United States under Emergency Use Authorization (EUA) and is also in phase 3 studies in hospitalized adults but is not available by eIND at present. Single doses of IV peramivir are as effective as a standard 5-day course of oral oseltamivir in outpatients, and it is already approved for use in Japan, South Korea, and China. A small RCT found that single daily doses of 600mg appeared to be more effective than 300mg in high-risk patients. Peramivir retains activity for some oseltamivir-resistant variants (e.g., Glu119Val) but is much less active (≥50-fold reduced susceptibility) for oseltamivir-resistant A(H1N1) viruses with the His275Tyr mutation, and a RCT found IV peramivir to be no more active for such infections than oseltamivir. Consequently, peramivir should not be considered as a reliable therapeutic option in such infections, until more data are available.

  • IV oseltamivir (Roche) at dose levels chosen to provide oseltamivir carboxylate levels comparable to those achieved by oral administration is also under development and is available on compassionate use basis.

Inhaled neuraminidase inhibitors

  • For patients who are intubated, use of the commercial zanamivir delivery device is not feasible. Nebulization of the licensed powder formulation, which contains lactose, is inadvisable, because it can clog ventilator tubing and filters and cause dangerous, potentially lethal dysfunction. The aqueous formulation used for IV administration is an investigational option for nebulization, but IV zanamivir would make more sense in mechanically ventilated patients.

  • Single doses of an inhaled long-acting NAI, called laninamivir (Daiichi-Sankyo, Biota), appear as effective as a 5-day course of oseltamivir in treating uncomplicated influenza in adults and children and are more effective in oseltamivir-resistant seasonal A(H1N1) infections in children, although not in adults for unclear reasons. Inhaled laninamivir is approved for use in Japan and is in clinical development in the United States and elsewhere.

Adamantanes (M2 ion channel inhibitors)—amantadine, rimantadine

  • Early amantadine and rimantadine therapy (≤2 days after illness onset) reduces the duration of uncomplicated influenza illness due to susceptible seasonal or pandemic influenza A strains. These drugs are inactive for influenza B viruses and resistance emerges rapidly during therapeutic use (approximately 30% frequency in outpatients and up to 80% in hospitalized children). The extent to which adamantane treatment might reduce the risk of complications or possibly benefit established treatments is uncertain. Rimantadine, approved in the United States, Russia, and other countries of the former Soviet Union, has the advantage of a lower risk of central nervous system (CNS) toxicities and less complicated dose adjustment in renal insufficiency compared with amantadine.

Antiviral resistance

  • Adamantane resistance is due to single amino acid substitutions in the target M2 ion channel protein and is high-level, leading to loss of antiviral and clinical effectiveness for both amantadine and rimantadine. The most common mutation Ser31Asn emerged in circulating A(H3N2) viruses in 2003 and rapidly spread globally to replace susceptible virus. At present, virtually all A(H3N2), A(H1N1)pdm09, avaian A(H7N9), as well as a majority of avian A(H5N1) (except for some clade 2.2 and 2.3) viruses harbor this mutation and are resistant. Consequently, amantadine and rimantadine are not recommended for antiviral treatment or chemoprophylaxis of currently circulating strains. Exceptions would be the use of an adamantane in conjunction with oseltamivir for treating suspected susceptible avian A(H5N1) illness, in context of controlled clinical studies of multi-drug combinations, or if oseltamivir-resistant but adamantane-susceptible strains of seasonal A(H1N1) virus were to re-emerge.

Investigational agents

  • In addition to investigational NAIs, several drugs or biologicals with novel mechanisms of antiviral action are in advanced clinical development and/or available on compassionate use (eIND in the United States) basis. Several might be considered for treatment of patients with serious infections due to multiply drug-resistant (both NAIs and adamantanes) strains. Whenever possible, patients should be enrolled into the RCTs assessing these agents.

    • Viral RNA polymerase inhibitors are inhibitory for both influenza A and B viruses and include ribavirin (Valeant plus others for oral formulation), which has been given by aerosol, oral, and intravenous routes for treating influenza; oral favipiravir (also designated T-705; Toyama), which has completed a phase 3 study in uncomplicated influenza in Japanese adults in which favipiravir showed antiviral effects comparable to oseltamivir and is under study in the United States; and others in earlier development.

      • Of these, oral ribavirin is approved for combination therapy of chronic hepatitis C and, hence, is readily available. Oral doses of 1g/day were ineffective in uncomplicated influenza but higher doses may have antiviral effects. IV ribavirin has been used in seriously ill influenza patients with some limited evidence for antiviral effects. Both formulations are associated with adverse effects, particularly hemolytic anemia, and risk of teratogenicity. Aerosolized ribavirin, approved for therapy of respiratory syncytial virus infections, has shown some clinical effectiveness in small controlled studies in uncomplicated influenza but is difficult and costly to administer. Oral favipiravir is not currently available for compassionate use.

    • Oral inhalation of the HA receptor-destroying sialidase construct DAS181 (Nexbio) has shown some antiviral activity in phase 2 studies in uncomplicated influenza; further studies are in progress, and it is available on compassionate use basis for treating complicated influenza A or B and parainfluenza virus infections. AVI-7100 (AVI BioPharma) is a small interfering RNA targeted to the gene encoding M and M2 proteins of influenza A viruses. It is active given topically or systemically in animal models and is undergoing phase 1 trials at present.

  • Convalescent plasma with increased titers of specific neutralizing antibodies has been used with apparent benefit in patients with critical illness due to avian A(H5N1) or A(H1N1)pdm09 virus infection who were also receiving NAI therapy. A small RCT of hyperimmune globulin found a significant survival benefit in critically ill A(H1N1)pdm09 patients given NAI therapy compared to IVIg lacking neutralizing antibody, if administered within 5 days of onset. A National Institute of Allergy and Infectious Diseases (NIAID)-sponsored RCT of adding pandemic H1N1 convalescent plasma to standard of care therapy in hospitalized patients is in progress.

  • Broadly reactive anti-HA human monoclonal antibodies that target conserved epitopes present on the HA stalk region and are inhibitory for multiple HA subtypes have been identified by several groups and are entering into clinical study. Monoclonals to other influenza targets on the virion surface (NA, ectodomain of M2) are also in development.

  • The oral antiparasitic agent nitazoxanide (Romark) is reported to have both interferon-inducing and other immunomodulatory properties, as well as to inhibit maturation of influenza HA. A recent RCT reported antiviral and clinical benefits in uncomplicated influenza at doses of 600mg twice daily for 5 days, and a phase 3 RCT of nitazoxnide given alone or in combination with oseltamivir has been initiated.

  • Intranasal interferon is not protective against human influenza; systemic or inhaled interferons have not been studied in human influenza but may be of future interest.

Antiviral combinations

  • Combinations of influenza antivirals have received preclinical study for decades as a means to enhance potency and reduce resistance emergence, but few controlled clinical trials have been undertaken. When the infecting virus is susceptible to adamantanes, their combined use with NAIs or ribavirin generally shows synergistic effects (hence the recommendation for using an adamantane with oseltamivir in treating certain A(H5N1) infections), but when the virus is adamantane resistant, no advantage of using the dual combination has usually been observed in most in vitro and animal model studies. Ribavirin and oseltamivir show enhanced, largely additive antiviral activity, whereas combinations of favipiravir with NAIs show synergistic effects in such preclinical studies.

  • One triple drug regimen of amantadine, ribavirin, and oseltamivir (TCAD, Adamas) shows synergistic activity for susceptible strains and also those with resistance to adamantanes (i.e., A(H1N1)pdm09) or oseltamivir (i.e., A/Brisbane/59/07(H1N1)) in preclinical studies. TCAD has been given to limited numbers of seriously ill HSCT patients with acceptable tolerability and pharmacokinetics, and one observational trial of mechanically ventilated A(H1N1)pdm09 patients found acceptable tolerance and a non-significant reduction in mortality compared to oseltamivir monotherapy. An NIAID-sponsored RCT that compares TCAD with oseltamivir monotherapy in ambulatory high-risk patients is in progress.

  • Depending on drug concentrations, combinations of zanamivir and oseltamivir show additive to antagonistic effects in in vitro studies, and one RCT in uncomplicated seasonal influenza (mostly A(H3N2) found the combination of oseltamivir and inhaled zanamivir to be inferior to oseltamivir alone. One small observational report found that the virologic response in critically ill A(H1N1)pdm09 patients on oseltamivir appeared to be somewhat better when the patients were switched to IV zanamivir than when IV zanamivir was added in combination. Until further data become available, combinations of these NAIs should be used in the context of controlled trials.

Supportive care


  • Antibiotic plus antiviral therapies are advisable for patients presenting with community acquired pneumonia (CAP) when influenza infection is also possible (e.g., during the influenza season). Empiric antibiotic coverage in those with pneumonia should include the most commonly recognized bacterial pathogens complicating influenza: Streptococcus pneumoniae, Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), S. pyogenes, and Haemophilus influenzae. Antibiotics are also necessary for treating influenza-associated bacterial complications at other sites (e.g., otitis media, sinusitis), although accurate clinical diagnosis is often difficult.

Antipyretics, analgesics

  • Over-the-counter drugs with antipyretic and analgesic properties (acetaminophen, ibuprofen, and other nonsteroidal anti-inflammatory drugs [NSAIDs]) are commonly used in influenza sufferers.

  • In addition to symptom relief, fever reduction with acetaminophen has been advocated for pregnant women with influenza to reduce the potential risk of teratogenic effects related to fever itself.

  • Salicylates should be avoided in children because of the association with Reye syndrome. In addition, high salicylate doses appeared to be associated with worse outcomes during the 1918 pandemic, and a possible association between certain NSAIDs and influenza-associated encephalopathy in children has been postulated.

Immunomodulators, corticosteroids

  • The role of widely available immunomodulators in treating influenza and its complications, such as acute lung injury, acute respiratory distress syndrome (ARDS), and sepsis syndrome, remains unclear. Systemic corticosteroids were used frequently in those with A(H1N1)pdm09-associated pneumonia or ARDS but appear to have caused increased risks of death, prolonged ventilatory support, nosocomial infections, including pneumonia, and corticosteroid-associated complications in intensive care patients. Systemic corticosteroids have also been associated with delayed cessation of influenza replication, and their use in influenza patients should be restricted to management of underlying medical conditions (outside of controlled clinical studies).

    • A variety of other immunomodulatory agents have been proposed for influenza treatment, some of which show beneficial effects in animal models (e.g., cyclo-oxygenase 2 inhibitors, glitazones, fibrates) or in epidemiologic (statins) studies of influenza. Although some retrospective data suggest that patients who were receiving statins (type and dose not specified) had reduced mortality when they were subsequently hospitalized with influenza, results are inconsistent across studies. Furthermore, it is currently unknown whether initiating use at time of influenza hospitalization or earlier in acute influenza illness is beneficial; controlled clinical studies are needed.

Ventilatory support

  • Respiratory failure with severe hypoxemia has been notable in patients hospitalized with influenza-associated pneumonia or exacerbation of underlying airways disease. In addition to administering supplemental oxygen and bronchodilators as indicated, prolonged mechanical ventilation has been required in most patients with viral pneumonia progressing to acute lung injury or ARDS. Extracorporeal membrane oxygenation (ECMO) has been reported as life-saving in some patients with ARDS.

How do patients contract this infection, and how do I prevent spread to other patients?


  • Influenza viruses frequently cause seasonal and very uncommonly zoonotic or pandemic infections in humans. Human influenza A and B viruses are circulating somewhere in the world at all times, and, additionally, the risk of zoonotic infection exists in countries where outbreaks of animal influenza are occurring (e.g., avian A(H5N1) or A(H7N9) in poultry). Consequently, travelers to affected areas need to take appropriate precautions to avoid exposures (use good hand hygiene, follow food safety practices, and avoid contact with animals or live markets) and be up-to-date with seasonal immunization.

Antigenic changes

  • The changing antigenicity of seasonal influenza viruses enables sustained circulation in human populations. Relatively minor changes, called antigenic drift, result from point mutations in HA and/or NA. The segmented genome allows for re-assortment of genes during dual infections; such re-assortment events contribute to both the origin of pandemic strains of influenza A and to the evolution and genetic diversity of seasonal strains.

  • For influenza A viruses, the unpredictable development of pandemic strains results from marked changes in HA with or without change in NA, called antigenic shift, due to the acquisition of new gene segments during re-assortment of human and animal viruses (e.g., A(H2N2) in 1957, A(H3N2) in 1968 or emergence of a novel animal influenza virus capable of sustained human-to-human transmission (e.g., swine-origin A(H1N1) in 2009. Furthermore, sporadic cross-species transmission of viruses circulating in animals (e.g., swine-origin A(H3N2), avian A(H9N2), A(H5N1), and A(H7N9)) cause antigenically distinct infections.

Seasonal influenza

  • Influenza viruses have a worldwide distribution and cause outbreaks of variable intensity each year. Because of human nfluenza's short incubation period (average 2 days, range 1-5 days), rapid onset and spread are characteristic in epidemics.

  • Seasonal influenza outbreaks typically occur during the winter months in temperate areas of the world. Circulation usually peaks between December and March in temperate Northern Hemisphere countries, but cases may occur earlier in autumn or later in spring. An opposite seasonal pattern occurs in the temperate areas of the Southern Hemisphere, where influenza circulates during summer months in the Northern Hemisphere.

  • Tropical and subtropical areas have variable patterns with year-round circulation and outbreaks often coinciding with rainy seasons. Annual double peaks of influenza activity have been described in several major Asian countries and cities (e.g., Bangkok, Hong Kong).

  • In a given locale in temperae regions, seasonal influenza epidemics typically last 6 to 8 weeks. The reasons for the distinct seasonality of annual influenza outbreaks in temperate regions are uncertain but likely multiple, including environmental, behavioral (e.g., indoor crowding), and perhaps population immunity (e.g., vitamin D levels, acquisition of specific immunity) factors. Low temperature and low humidity conditions help maintain influenze virus infectiousness in aerosols and in the environment; seasonal outbreaks in temperate areas have been linked to periods of low absolute humidty. Of note, pandemic influenza characteristically shows out-of-season circulation and often multiple waves.

Zoonotic infections

  • Influenza A viruses that circulate in animals may cross the species barrier to infect humans and cause sporadic illnesses (e.g., avian A(H5N1)). Rarely, such a virus may evolve to become a pandemic strain (e.g., A(H1N1)pdm09). Avian A(H5), A(H7), and A(H9) viruses have all caused human infections during the past 20 years. The process of host species switching is not well understood and may be unique to each particular virus.

Recent animal-origin influenza outbreaks

  • From 2005 to 2011 several dozen swine-origin A(H1N1 or H1N2) or A(H3N2) infections were reported in the United States. In 2012 a novel swine-origin, triple reassortment A(H3N2) virus that possesses the M gene from A(H1N1)pdm09 caused over 300 hundred infections in multiple states of the United States, principally in children. Severity has been comparable to seasonal A(H3N2) illness, including some hospitalizations and at least one death. The major risk factor has been swine exposure in the context of agricultural fairs and events, and avoidance of swine exposure, particularly in those at increased risk of influenza complications, is warranted. However, several clusters and lack of swine exposure in some cases indicate human-human transmission, presumably due to nonsustained household or community transmission. The possibility exists that more efficient and wider spread circulation could develop. When isolated from humans, these novel strains are now referred to as "variant influenza viruses" and designated by the letter "v" (e.g., A(H3N2)v); the corresponding swine viruses containing the influenza A(H1N1)pdm09 virus M gene are referred to as H3N2pM virus. Recent human cases of swine-origin A(H1N1)v or A(H1N2)v have also been described.

  • On 31 March 2013 Chinese authorities alerted WHO of three human infections with an avian influenza A(H7N9) virus not previously reported in humans. Retrospective studies documented human infections in eastern China as early as February 2013, and other 130 proven cases with high case-fatality have been confirmed to mid-May 2013.

    • Sequence analyses indicated that all the genes were of avian origin and resulted from reassortment of multiple avian viruses, with the H7 derived from viruses in domestic ducks, the N9 from viruses in wild birds, andthe six internal genes probably originating from two different groupsof avian A(H9N2) viruses in chickens.

    • The human isolates possess mutations indicative of mammalian adaptation including those that increase binding of virus to human cell receptors, increase replication at temperatures present in the upper respiratory tract, and increased replication, virulence, and respiratory droplet transmissibility in experimental mammalian models.

    • Ducks and chickens probably acted as the intermediate hosts leading to its emergence. Virus has been infrequently detected in poultry, other birds, and environmental samples of live animal markets, but not in swine to date. Unlike avian (A(H5N1) viruses, the novel (A(H7N9) virus has low pathogenecity for chickens, and poultry infections do not cause disease outbreaks that might serve to indicate its presence.

    • Almost all confirmed human cases have been sporadic and are presumed to have resulted from exposure to infected birds or their environments. Of the first 82 proven cases, 77% reported exposure to live animals, primarily chickens (76%) and ducks (20%). with closure of live bird markets in affected areas, the number of new cases declined quickly in late April.

    • Unlike avian A(H5N1) cases, most of those affected have been older adults (median age, 61 years), male (71%), and urban residents (84%), perhaps related to behaviors that increase the risk of severe disease. About three-quarters have had at least one underlying health condition. Human-to-human virus transmission has not been documented among close contacts, but such transmission may have occurred in several family clusters. The animal reservoirs of the virus and whether the virus will continue to cause sporadic human cases or possibly evolve to one capable of sustained community transmission remain to be seen.

Detection of novel strains

  • The evaluation of patients with unexplained febrile respiratory illness, particularly those hospitalized with more severe manifestations, should include a careful epidemiologic history regarding potential exposures (e.g., recent exposures to swine, birds, other ill animals; attendance at agricultural events; recent travel to risk areas for avian A(H5N1) or A(H7N9) or places where outbreaks of influenza are occurring; visiting or living in facilities or households where outbreaks are occurring).

  • Clinicians should consider the possibility of avian A(H7N9) or A(H5N1) virus infection in patients with illness compatible with influenza who (1) have traveled with ≤ 10 days of illness onset to countries where the virus has been detected in humans or animals,or (2) have had recent contact (within ≤ 10 days of illness onset) with a person confirmed to have infection with an avian influenza virus.

  • When concerned about possible zoonotic infection, virologic studies to detect novel strains should be undertaken. More detailed virologic studies in reference laboratories are also indicated when influenza viruses are found that are not typable with standard methods.

Pandemic influenza

  • Although the precise definition of pandemic influenza is debated, the term generally refers to a world-wide epidemic due to a novel strain possessing genes of animal origin for which most persons lack immunity and which transmits readily from person-to-person, often outside of the usual seasonal patterns. Consequently, a pandemic causes illness in all or most age groups. As shown by the experience with A(H1N1) pandemics and pandemic-like events (1918, re-emergence of A/USSR/77(H1N1) in 1977, and A(H1N1)pdm09 in 2009), the virulence of pandemic strains ranges widely. This and other factors affect the impact at the population level. Once pandemic strains emerge, they continue to circulate globally until most susceptibles are exhausted and then undergo antigenic drift, so that progeny viruses continue to cause seasonal epidemics.

Routes of transmission

  • Virus expelled in respiratory secretions, particularly during coughing, sneezing, or talking, is the transmission source of seasonal and pandemic influenza virus infections. Of note, presymptomatic transmission has been reported, but its frequency is uncertain. Zoonotic infections may occur after contact with infected animals, their excretions, or possibly ingestion of contaminated undercooked food or water (avian H5N1). Multiple routes of influenza virus transmission are possible (direct, large droplets, small particle aerosols, hand contamination from fomites and self-inoculation), and their relative importance in different situations remains to be clarified. Available evidence from diverse study settings suggests that interventions to protect against airborne droplets and hand hygiene both reduce risk of acquisition.

  • Viral infectivity is lost rapidly on porous surfaces and hands but may be retained for days on nonporous surfaces, particularly when protected by secretions and in low humidity and temperature conditions. The virus can remain infectious for 24 hours or more after aerosolization under conditions of low (25%) or high relative humidity (80%) but is less stable at intermediate relative humidity.

Incidence and impact

Seasonal influenza

  • Seasonal influenza infections are very common and are estimated to affect approximately 10% of adults and, depending on age, up to 20 to 30% of children each year. In the United States, an average of more than 200,000 influenza-related hospitalizations and approximately 24,000 deaths have occurred annually during recent years, although the range across years varies more than ten-fold, depending on the circulating viruses and affected age groups. During seasonal outbreaks, the highest rates of hospitalization are in young children, but most influenza-associated deaths (more than 85-90%) occur in those aged 65 years or older. Globally, more than 500,000 persons are estimated to die from influenza and its complications each year.

Avian influenza infections

  • Avian A(H5N1) viruses continue to cause rare human infections (more than 625 infections documented to April 2013) associated with high mortality (approximately 60%). The most commonly identified risk factor has been exposure to sick or dying poultry. Limited chains of human-human transmission have been found in several family clusters and health care worker (HCW) infections. These viruses also continue to evolve genetically and antigenically and are entrenched in poultry populations in multiple Asian countries (i.e., Indonesia, China, Vietnam, Cambodia, and Bangladesh) and in Egypt. Recent laboratory-based studies indicate that for several A(H5N1) viruses, a small number of mutations, primarily in HA, can lead to strains that are transmissible by airborne spread between ferrets (thought to be a predictive model for human transmissibility).Avian A(H5N1) viruses possessing one or several of these mutations already exist in nature.

  • Sporoadic zoonotic infections due to avian A(H7N3), A(H7N7), A(H7N2), or A(H9N2) viruses have been recognized over the past 20 years. Most of these have been associated with conjunctivitis and/or ILI. One poultry outbreak of highly pathogenic A(H7N7) virus in Holland in 2003 was associated with 89 documented human infections, including one fatality, and evidence for limited human-to-human transmission.

  • Approximately 130 proven human cases of avian A(H7N9) with case-fatality exeeding 25% have been confirmed to mid-May 2013. Although sustained human-human transmission of avian A(H7N9) virus has not occurred to date, an obvious concern is that this virus could evolve to one capable of global spread. Rare human infections by avian A(H7N9) virus were found in initial ILI surveillance in affected areas in March-April 2013 (0.03% of over 20,000 tested). Although the number of human infections has rapidly diminished due to public health measures to diminish human exposures, particularly closure of live bird markets, the future direction of this outbreak is uncertain. The extent of avian A(H7N9) infection in poultry, wild birds, and other animals is under investigation. Avian influenza infections are typically more prevalent in poultry during the cool weather months of the year with the potential for more human cases.

Pandemic influenza

  • The impact of influenza pandemics ranges widely and depends on the virulence of the circulating strains, population immunity (particularly in older adults) related to earlier exposure to antigenically related viruses, population prevalence of risk factors (e.g., malnutrition, cardiopulmonary conditions), and rapid access to health care and specific pharmaceutical interventions (i.e., antivirals, antibiotics, intensive care support, and vaccines).

    • Compared to seasonal epidemics, pandemics are notable for excess complications and mortality in children and young adults, particularly in certain risk groups. Of note, the excess mortality that occurs in those aged younger than 65 years may continue for up to a decade after introduction of a pandemic virus. The three waves of the 1918 pandemic are estimated to have caused over 675,000 deaths in the United States and more than 40 million deaths globally, although the mortality rates varied about four-fold by state and 40-fold by country, with high mortality in south Asia. More than 90% of these deaths occurred in those aged younger than 65 years.

    • During its first year of circulation in the United States, the A(H1N1)pdm09 virus was associated with an estimated 60 million cases, 275,000 hospitalizations, and 12,000 or more deaths; the rates of influenza-associated hospitalization and death increased four- to 12-fold in children and young adults, compared with seasonal rates but decreased four- to five-fold in those aged 65 years or older. Globally an estimated 150,000-575,000 respiratory and cardiovascular deaths occurred, with 80% of these in persons less than 65 years old.

Infection control issues

  • Infection control to reduce influenza transmission includes not only acute and chronic health care facilities, but also household and community settings. Specific immunization remains the primary means of prevention, but nonpharmaceutical interventions (e.g., hand hygiene, cough etiquette, isolation of ill persons, school closures, other social distancing tactics, personal protective equipment) and antiviral chemoprophylaxis are important adjunctive strategies. The following comments focus on high-risk patients and healthcare settings. Updated advice is available through the CDC and WHO websites.

Patient isolation and management

  • Patients hospitalized with suspected or proven seasonal influenza should be managed with standard and droplet precautions, including use of single rooms whenever possible. Those hospitalized with A(H5N1), A(H7N9), or other novel strains of uncertain virulence and transmissibility should also be managed with airborne and contact precautions, including eye protection (goggles or face shields). Aerosol-generating procedures (e.g., bronchoscopy, intubation, and sputum induction) should be done in airborne isolation (negative pressure with frequent air changes and high-efficiency particulate air [HEPA] filter exhaust). Cohorting of patients with documented influenza may be necessary during high demand periods. Visitors should be limited in general and prohibited if ill.

  • Aerosol-generating procedures (e.g., bronchoscopy, intubation, and sputum induction) should be done in airborne isolation environments (negative pressure with frequent air changes and high-efficiency particulate air [HEPA] filter exhaust) with appropriate precautions for healthcare workers.

  • Cohorting of patients with documented influenza may be necessary during high demand periods. Visitors should be limited in general and prohibited if ill.

  • Source control. Whenever feasible, masking of suspected or proven influenza patients in healthcare settings (e.g., emergency department, during transport, in diagnostic facilities) is warranted to reduce environmental contamination by infectious droplets and transmission to contacts.

  • Disinfection. Standard disinfection procedures are adequate. Influenza viruses are enveloped viruses and susceptible to agents that affect membranes, including ionic and nonionic detergents, chlorination, and organic solvents.

  • Personal protective equipment for HCWs. Very limited data suggest that masks may be as effective as respirators (N-95 or equivalent) in protecting HCWs from seasonal influenza during routine care, but further studies are needed. Potentially infectious small particle aerosols can be detected within about 6 feet of influenza patients, and compliance with fit-tested respiratory is likely to provide higher levels of protection. Respirators and eye protection (i.e., goggles or face shields) should be used for aerosol-generating procedures. Compliance with masking and hand hygiene also appears to somewhat reduce influenza transmission in dormitories and household settings.

  • Ill HCWs. Effective management of ill HCWs is key to reducing the risk of nosocomial transmission. In addition to seeking appropriate care, those with new onset of respiratory illness should not report to work, or, if illness develops on the job, stop patient care, mask, and avoid exposing others. Like other immunocompetent adults, ill HCWs can be positive for infectious virus and, hence, potentially infectious for others, in absence of fever at presentation or sometimes after defervescence.

  • Immunization. Since 2010 in the United States, annual influenza vaccination has been recommended for all persons aged 6 months and older who do not have contraindications. HCWs have been a long-standing target group for immunization, and several professional societies (e.g., Infectious Diseases Society of America, Society for Healthcare Epidemiology of America) advocate mandatory HCW immunization because of its importance in patient safety. An increasing proportion of medical centers in the United States are making annual influenza immunization a condition of employment. Current seasonal vaccines are trivalent (antigens for A(H1), A(H3), and B strains), and their composition is determined approximately 8 months before their deployment in the autumn. Consequently, antigenic mismatches with circulating strains and decreased effectiveness occur in some seasons. One quadrivalent seasonal vaccine (containing antigens for 2 A and 2 B strains has been approved but not yet marketed).

    • Most current seasonal vaccines are trivalent (antigens for A(H1), A(H3), and B strains), and their composition is determined approximately 8 months before their deployment in the autumn. Consequently, antigenic mismatches with circulating strains and decreased effectiveness occur in some seasons. Quadrivalent live-attentuated and inactivated seasonal vaccines (containing antigens for 2 A and 2 B strains) have been approved and are expected to be available from the 2013-14 season.

    • Unimmunized patients hospitalized before or during the influenza season should be given inactivated influenza vaccine before or at the time of hospital discharge.

    • Vaccine selection for HCWs. Multiple vaccine types and routes of administration are now available (e.g., standard inactivated intramuscular, high-dose inactivated intramuscular for elderly, inactivated intradermal, intranasal live-attenuated for nonrisk people aged 2-49 years). The live-attenuated influenza vaccine (LAIV) appears less protective overall in adults than intramuscular inactivated TIV and should not be used in HCWs who might be in contact with severely immunocompromised hosts during the week after its administration. All currently available vaccines are egg-grown vaccines; desensitization is possible in those with serious anaphylactic egg allergy, and investigational cell culture-grown vaccines are in advanced development.

    • Most currently available vaccines are egg-grown vaccines; desensitization is possible in those with serious anaphylactic egg allergy. However, recently approved recombinant HA-based vaccine grown in insect cells and cell culture-grown vaccines are available for use in egg-allergic persons.

  • Antiviral chemoprophylaxis. Both inhaled zanamivir and oral oseltamivir given once daily are effective for prophylaxis of influenza A and B virus infections (see Table I for dose regimens). The adamantanes given once daily are also effective prophylaxis when the implicated influenza A strain is susceptible. However, when used for both index case treatment and postexposure prophylaxis of contacts in households, adamantanes are not effective prophylactically because of rapid emergence and transmission of resistant variants, so that use should be restricted to prophylaxis under such circumstances.

    • Outbreak control. When used in households for postexposure prophylaxis, the efficacy of NAIs in preventing influenza illness in adults is approximately 70 to 80%, but lower in young children. Both zanamivir and oseltamivir have been used for outbreak control in healthcare settings. In such situations, prophylaxis of both patients and HCWs, irrespective of vaccine status, makes sense. The recommended duration of chemoprophylaxis depends on the clinical situation but is generally 7 to 10 days for postexposure prophylaxis and in outbreaks is for 2 weeks or at least 1 week after the last case, whichever is longer.

    • For postexposure prophylaxis in immunocompromised hosts, use of standard treatment dose regimens (i.e., twice daily administration) is warranted in efforts to reduce the risk of resistance emergence.

    • When new cases develop despite oseltamivir prophylaxis, particularly in high-risk units of immunocompromised patients or severely ill patients, concern heightens regarding possible transmission of oseltamivir-resistant virus and the need for a switch to inhaled zanamivir prophylaxis.

    • Seasonal prophylaxis. These agents are highly effective for pre-exposure prophylaxis during sustained use across the influenza season (4-6 weeks), including in nonimmunized persons. One 12-week oseltamivir study in immunocompromised hosts found good tolerance and effectiveness against laboratory-proven influenza illness. Long-term prophylaxis is an option in high-risk patients who might not respond to immunization (e.g., recent HSCT or SOT recipients) or when the vaccine is unavailable or poorly matched antigenically.

What host factors protect against this infection?

  • All arms of the immune system contribute to either prevention of infection and/or mitigation of its severity. Protection against infection has been correlated with the levels of neutralizing and HAI antibodies in the blood and respiratory secretions.

    • Current inactivated vaccines for seasonal influenza are based on attaining minimum thresholds of serum HAI antibodies thought to confer protection (generally HAI ≥1:40) in recipients. Antibodies to other viral proteins such as NA and the ectodomain of matrix protein 2 (M2e) also moderate viral replication, but humoral responses do not appear until after the first week of infection.

    • Cellular immune responses, particularly virus-specific cluster of differentiation (CD)8+ T-cell ones, occur earlier. One recent study found that re-existing CD4+, but not CD8+, T cells responding to conserved epitopes on influenza internal proteins were associated with lower virus shedding and less severe illness in experimentally infected volunteers. Although these T-cell responses do not prevent infection, they contribute to controlling replication by destroying virus-infected cells.

    • Highly immunosuppressed hosts (particularly HSCT), solid organ transplant recipients with lymphopenia, and acute leukemia or oncology patients on intensive chemotherapy, can experience protracted viral replication and high frequencies of lower respiratory complications. This may occur despite initial presentation with apparently mild illness.

    • Innate immune responses (e.g., interferons, other cytokines and chemokines, components of respiratory secretions like surfactants, natural killer cells) are likely quite important in modulating the extent of viral replication early in the course of illness. Deficient interferon responses have been reported in some patients with severe influenza viral pneumonia.

  • The risk of infection depends primarily on exposure to influenza-infected persons or, in the case of zoonotic infections, infected poultry or swine or their environments, and on host immunity related to prior influenza infection and/or specific immunizations. Once infected, the likelihood of illness depends on the infecting virus strain, viral inoculum and site of deposition, and various host factors including immune status.

  • Persons at higher risk for influenza complications (adapted from CDC advice) include:

    • residents of nursing homes and other chronic-care facilities

    • children aged younger than 5 years (particularly those aged younger than 2 years); adults aged 65 years or older

    • persons with chronic pulmonary (including asthma), cardiovascular (except hypertension alone), renal, hepatic, hematologic (including sickle cell disease), metabolic disorders (including diabetes) or neurologic or neurodevelopmental conditions (including cerebral palsy, seizure disorders, stroke, mental retardation, moderate to severe developmental delay, muscular dystrophy, or spinal cord injury)

    • persons with immunosuppression, including that caused by medications, malignancy, or by human immunodeficiency virus infection

    • women who are pregnant or postpartum (within 2 weeks after delivery)

    • persons aged 18 years or younger who are receiving long-term aspirin therapy

    • American Indians/Alaska Natives

    • persons who are morbidly obese (i.e., body mass index ≥40; note that the risk of complications likely increases at even lower levels of obesity)

  • In those hospitalized with pandemic 2009 H1N1 illness, approximately 80% of adults and 40 to 60% of children have had underlying conditions, with asthma being the most common underlying condition in children.

  • Influenza viruses can infect all levels of the respiratory tract, and bronchial biopsies taken from those with apparently uncomplicated influenza show degeneration of respiratory epithelial cells with loss of ciliated tufts and desquamation, as well as inflammatory changes, including mononuclear cell infiltrates in the lamina propria. Hemorrhagic, airless lungs and severe tracheobrobchitis are characteristic in those dying of viral pneumonia. The histopathologic hallmark is diffuse alveolar damage, which is accompanied by varying degrees of necrotizing tracheobronchitis, intra-alveolar hemorrhage and exudation, hyaline membrane formation, and mononuclear cell infiltration with later changes of metaplastic regeneration and fibrosis. Extensive neutrophilic infiltrates are typically present in those with secondary bacterial pneumonia.

What are the clinical manifestations of infection with this organism?

  • Influenza virus infections and their complications cause a wide variety of clinical syndromes, ranging in severity from mild common colds to influenzal illness to fatal disease due to respiratory failure, often with multisystem organ failure (MOF). Infections often cause exacerbation of underlying conditions.

  • The incubation period of seasonal influenza is about 2 days (range 1-6 days) but may be longer in zoonotic infections.

  • All three influenza types can cause typical influenza illness, as do many other respiratory viruses. Depending on the particular virus and host, most illnesses due to seasonal influenza strains are self-limited and up to 50% are subclinical (based on serology).

  • Influenzal illness is typically manifested by acute onset of systemic symptoms (i.e., fever, chills, fatigue, lassitude, myalgia, headache) concurrently with or followed shortly by respiratory complaints (i.e., sore throat, cough, coryza, tracheal discomfort). Often influenza will lack one or more typical symptoms, but cough is characteristic.

  • Manifestations vary by age group with older adults having higher frequencies of altered mental status and gastrointestinal complaints and less fever and myalgia.

  • When used for epidemiologic purposes, influenza-like illness (ILI) is often defined by constellation of fever with sore throat alone or cough, although sore throat has been a negative predictor of influenza in several studies.

  • When influenza is prevalent in a given locale, the presence of documented fever and cough is highly predictive for influenza infection in adults (up to approximately 80%), although much less so in children (approximately 40%) in whom other respiratory viruses cause similar manifestations or in hospitalized patients.

What common complications are associated with infection with this pathogen?

  • Respiratory complications. Influenza infections are associated with a wide range of complications affecting the upper (sinusitis, otitis media) and lower (bronchitis, pneumonia, and in children bronchiolitis and laryngotracheobronchitis [croup]) respiratory tracts. Tracheobronchitis is so common in patients presenting for care that may be considered part of the influenzal syndrome. These complications can be due to direct viral infection, secondary bacterial infections, or a mixed process. The distinction is very difficult without proper microbiologic studies. One study during the 2009 pandemic found that the absence of crackles on auscultation and presence of oxygen saturation greater than 96% on room air predicted the absence of pulmonary infiltrates on chest radiograph.

  • Other complications. Secondary bacterial complications are usually due to S. pneumonie,S. aureus including MRSA, S. pyogenes, and H. influenzae and uncommonly include severe toxigenic S.aureus or S. pyogenes, or invasive meningococcal infections. Invasive aspergillosis occurs rarely. Other complications linked to viral infection and/or host proinflammatory responses include rhabdomyolysis, myocarditis, myocardial infarction, cardiac arrhythmias, various CNS syndromes (febrile seizures, encephalopathy, meningoencephalitis, transverse myelitis, Guillain-Barré syndrome, Reye syndrome, possibly narcolepsy), renal failure, sepsis syndrome with MOF, disseminated intravascular coagulopathy, and hemophagocytic syndrome. In seriously ill patients a range of nosocomial complications including ventilator-associated pneumonia and thromboembolic events may develop.

  • Influenza infections during pregnancy, particularly during the second and third trimesters, are associated with increased risk of maternal complications and mortality, fetal loss, and premature delivery.

  • Causes of hospitalization. In adults, the most common causes for hospitalization with influenza are exacerbations of underlying conditions, particularly ischemic cardiovascular disease, congestion heart failure, asthma, chronic obstructive pulmonary disease, and diabetes. Pneumonia is documented in approximately 30% of hospitalized adults with seasonal influenza and includes primary viral, secondary bacterial, and mixed viral-bacterial types.

    • During A(H1N1)pdm09 infection, the most common cause of ICU admission was progressive viral pneumonia and lung injury leading to ARDS. Approximately 30% of severe or fatal A(H1N1)pdm09 cases had bacterial coinfections detected at the time of hospitalization or ICU admission (compared with >90% of fatal 1918 pandemic cases when antibiotics were not available). Both seasonal influenza, particularly A(H3N2) epidemics and the A(H1N1)pdm09 pandemic were associated with increases in invasive S. pneumonie and S. aureus infections, including MRSA infections, particularly in children and young adults. In children hospitalized with seasonal or pandemic 2009 H1N1 illness, the most common cause has been asthma exacerbation.

    • Avian A(H5N1) and A(H7N9) viruses have caused high rates of progressive viral pneumonia leading to respiratory insufficiency, ARDS, and often multi-organ dysfunction. In the recent avian A(H7N9) outbreak the incubation period has been estimated to range from 1-10 days (median, 6 days), and most patients have presented with fever, cough, and dyspnea. Almost all documented cases have been hospitalized with progressive pneumonia and often other organ dysfunction; about one-half have developed ARDS. The time from illness onset to ICU admission has been about 1 week (IQR, 5-9 days) and to death a median of 11 days (IQR, 7-20 days). Several mild or asymptomatic infections have been documented, primarily in children, and the full spectrum of disease remains to be determined.

How should I identify the organism?

Influenza replication cycle

  • Replication starts with attachment of the viral HA to sialic acid-bearing cellular receptors. After internalization into endosomes, acidic pH-mediated conformational change in the HA facilitates fusion of the viral and endosomal membranes. In conjunction with the ion channel function of the M2 protein (influenza A), which enables an influx of hydrogen ions into the virion interior, these early steps result in uncoating of the viral RNA segments and their release into the cytoplasm. Viral RNA is transported into the cell nucleus, where transcription to messenger RNA and replication of the viral genome are mediated by a viral RNA-dependent RNA polymerase. Translation of viral proteins follows in the cytoplasm, but viral polymerase, nucleoprotein, and other viral proteins return to the nucleus where they associate with viral RNAs before export back to the cytoplasm.

  • These newly synthesized viral RNA complexes assemble with the surface glycoproteins HA, and NA, and virus particles bud from the cyotplasmic membrane. Removal of sialic acids from the cell surface, virion itself, and respiratory secretions by NA is essential to preventing virus aggregation at the cell surface and allowing spread within the respiratory tract.

  • Multiple steps in influenza viral replication, including key interactions with various cellular pathways essential to viral replication, are potential targets for inhibitors, although to date only two antiviral classes, NAIs and M2 ion channel protein inhibitors, have well-established clinical utility.

Target groups for testing

  • Influenza diagnostic testing should generally be undertaken when the results will affect medical care or public health decision-making. Priority groups for testing include hospitalized patients and those at increased risk for progression to severe illness; those with possible zoonotic infections; and individuals involved in outbreaks, particularly in institutions, schools/camps, and travel groups.

  • More detailed virologic studies for possible novel strains should be considered when an isolate or viral RNA sample is not typable by standard reagents. The FDA-approved, CDC-developed reverse transcriptase-polymerase chain reaction (RT-PCR) assay that has been deployed to US state and WHO-affiliated laboratories can detect many novel viruses including the swine-origin A(H3N2)v and and avian viruses.

  • Specimens for diagnostics. A wide range of respiratory tract specimens are acceptable for diagnostic purposes. In patients with severe or progressive lower respiratory tract illness, multiple samples and particularly those from lower respiratory tract sites (e.g., sputum, tracheal aspirate, bronchoalveolar lavage) should be collected, as false-negative results on single upper respiratory tract specimens are common.

    • For upper respiratory specimens, a variety of sample types (e.g., nasopharyngeal aspirates, nasal washes, swabs, throat swabs and gargles) have been used for virus detection. Nasopharyngeal and nasal specimens generally have higher yields than throat, except for avian A(H5N1) infections in which throat swabs appear to provide greater yield. In general, nasopharyngeal aspirates, particularly in children, or a combination of nasopharyngeal and throat swabs provide samples with adequate yields for seasonal strains.

    • For all methods, collecting samples as early in the course of illness as possible (≤3 days after onset) will enhance yields, although later sampling is warranted for those hospitalized later in illness.

    • Of note, commercial rapid influenza diagnostic assays (RIDTs) have different specifications for acceptable specimen, and package inserts should be consulted.

  • Rapid influenza diagnostic tests. Commercially available, point-of-care diagnostic RIDTs can detect influenza antigens within 15 to 30 minutes with reasonably high specificity (90-95%) but only low to moderate sensitivity (approximately 40-70% in adults) compared with virus isolation or RNA detection. Tests do not distinguish influenza A subtypes, and the specificity of most assays (usually >90%) reduces their positive predictive value outside the influenza season. RIDTs that employ optical reading devices are approved and show higher analytic sensitivity.

    • Approximately one dozen commercial assays are available for use in the United States (see CDC website). Sensitivity depends on patient age (higher in children), duration of illness (highest on day 2 or 3 of illness), infecting virus (higher for influenza A than B; low for A/H5N1), and specimen type (lower in throat swabs). Consequently, negative results do not exclude influenza and should not be used to make individual patient treatment or infection control decisions. Limited sensitivity, averaging approximately 50 to 60% across studies but sometimes <20%, has been noted in adults. Furthermore, RIDTs vary widely in their analytic sensitivities and some fail to detect H3N2v viruses.

    • Because of their quick turn-around times, RIDTs can be useful in initial evaluation of outbreaks of unexplained febrile respiratory illness. False-positive results may occur, particularly during low prevalence periods of influenza, and positive RIDTs during such periods require further diagnostic testing. The US Food and Drug Administration (FDA)-approved RIDTs vary in complexity (Clinical Laboratory Improvement Amendments waived for any outpatient versus performance in moderately complex clinical laboratory tests) and in detection strategies (distinguishing between influenza A and B viruses).

    • None of the available RIDTs identifies specific influenza A subtypes or novel influenza viruses like H3N2v.

    • Direct or indirect immunoflourescence testing for influenza antigens is generally somewhat more sensitive than commercial RIDTs and is reasonably fast (1-4 hours), but requires samples with adequate cellularity, appropriate reagents, and experienced laboratory staff.

  • Virus isolation. Isolation of influenza virus is more sensitive and specific than RIDTs and can be accomplished with several different cell types (e.g., Madin-Darby canine kidney, primary monkey kidney, rhesus monkey kidney epithelial [LLC-MK2], Vero, mink lung cells) and embryonated hen's eggs. Although viral isolation is available in many laboratories, it generally requires 3 to 10 days (1-3 days for rapid culture assays or shell vials using immunofluoresence) and is both less sensitive and slower for diagnosis than detection of viral RNA by nucleic acid amplification testing (NAT). However, isolation of virus establishes the presence of active virus replication and remains important for both public health purposes (assessing presence of antigenic or novel strains, antiviral susceptibility patterns) and in individual patients with complicated courses (e.g., antiviral susceptibility testing in immunocompromised patients).

  • If short-term sample storage is necessary before processing, they can be held at refrigerator temperatures for 1 to 4 days. Freezing, particularly in standard -20oC freezers, of specimens causes loss of infectivity, whereas freezing at or below -70oC preserves infectivity.

  • Viral RNA detection. Nucleic acid amplification assays are currently the most accurate and sensitive tests for detecting influenza viruses, including A(H1N1)pdm09 and avian A(H5N1) or A(H7N9) viruses, and hence the current diagnostic tests of choice for influenza. RT-PCR test platforms that can subtype influenza A viruses, including novel strains, are available through the CDC and in state public health and some reference laboratories. Because of higher sensitivity and detection of noninfectious virions, RT-PCR positivity often lasts for several days longer than culture positivity and RNA copy numbers are approximately 100- to 1,000-fold higher than titers of infectious virus.

    • The CDC initially developed and distributed a real-time RT-PCR method for subtyping of multiple influenza A viruses, including pandemic A(H1N1)pdm09 virus (CDC FLU rRT-PCR Dx Panel influenza assay). Subsequently, commercial RT-PCR assays that can distinguish A(H1N1)pdm09 virus from other influenza A viruses have been FDA-approved, and a number of hospital or referral laboratories have developed validated in-house assays.

    • A new CDC-developed H7 test has been cleared by the Food and Drug Administration for use as an in vitro diagnostic test under an Emergency Use Authorization, and this CDC H7 rRT-PCR test is now available to all qualified U.S. public health and U.S.Department of Defense laboratories and WHO-recognized National Influenza Centrs globally.

    • Commercially available molecular assays do not differentiate H3N2v virus from seasonal influenza A (H3N2) virus, and the sensitivity and specificity of these assays to detect H3N2v virus are uncertain. With the CDC FLU rRT-PCR Dx Panel assay on respiratory specimens, positive results for influenza A, pandemic A, and H3 (Influenza A+, H1-, H3+, pandemic A+, pandemic H1-) are considered presumptive positive for H3N2v virus.

    • Multiplex assays that can detect a wide range of respiratory viruses with high sensitivity are commercially available (xTAG, Luminex; FilmArray, Idaho Technologies); the assay time from receipt of sample is generally 4 to 6 hours but can be as short as 1 hour. While their sensitivity varies with specific assay, their breadth of diagnostic coverage and relatively short turn-around time, generally 4-6 hours but sometimes as short as 1 hour, render such assays particularly valuable in seriously ill and immunocompromised hosts.

  • Serology. Serologic studies are not useful for rapid diagnosis of influenza, as paired acute and convalescent sera are usually required. However, it may provide retrospective diagnosis in challenging cases, although those dying early in illness course and severely immunocompromised hosts may not mount antibody responses. A variety of assay methods (i.e., HAI, enzyme-linked immunosorbent assay, neutralization) have been used and are preferable to the less sensitive complement fixation one.

How does this organism cause disease?

  • Illness pathogenesis. The initial site of viral deposition and principal location of replication is the respiratory tract. Viremia or extrapulmonary detection of infectious influenza virus is rare, although viral RNA in the blood, stool, and in some with CNS manifestations cerebrospinal fluid (CSF) can be found by RT-PCR. Higher blood levels of viral RNA, perhaps representing spill over from the lung, appear to correspond with more severe disease. Respiratory cell damage and loss are related to direct viral cytopathic effects, virus-induced apoptosis, and host proinflammatory mediator and cellular immune responses. Respiratory mucosal effects likely account for much of the associated respiratory complaints, particularly cough and tracheobronchitis.

    • Respiratory tract and systemic cytokine and chemokine responses are also important in illness pathogenesis, particularly fever and other systemic symptoms. Excessive responses are postulated to contribute to both local and systemic immunopathologic changes in those with severe pneumonia and multiorgan dysfunction.

    • In adults hospitalized with severe A(H1N1)pdm09 virus pneumonia, significantly increased blood proinflammatory cytokine responses but diminished adaptive immunity responses (Th1/Th17-related) were found in comparison to those hospitalized with seasonal influenza; these responses corresponded with some clinical outcomes (e.g., need for ICU admission).

    • In A(H5N1)-infected patients, available evidence indicates that blood concentrations of key proinflammatory mediators correlate with levels of virus in the upper respiratory tract, and high blood levels of various cytokines and chemokines have been reported in avian A(H5N1) and A(H7N9) patients.

    • Early deficiencies in key innate immune responses that help control replication, particularly interferons, and dysregulated T-cell responses have been found in severe influenza viral pneumonia. Prolonged viral replication may be associated with sustained high-levels of proinflammatory mediators. Such observations highlight the importance of controlling viral replication and also studying immunomodulatory interventions that either augment deficient or modulate excessive immune responses.

  • Viral factors

    • Receptor patterns. Cellular receptors for influenza viruses vary in type and distribution within different portions of the respiratory tract, but all have linkages to terminal sialic acid residues.

      • Human influenza viruses have preference for alpha-2,6-sialic acid linkages that predominate in receptors in the nasopharynx and tracheobronchial tree, whereas avian viruses like A(H5N1) target alpha-2,3-sialic acid linkages that are present on some cells the distal airways, alveoli, and conjunctivae. This may explain, in part, the high frequency of pneumonia in avian A(H5N1) and A(H7N9)-infected patients and the limited human-human transmissibility observed to date.

      • All pandemic influenza viruses to date have HA with alpha-2,6 receptor preference. In addition to HA, other viral genes such as PB2 can also affect transmissibility.

    • Viral virulence markers. Viral virulence correlates primarily with the magnitude and sites of viral replication in vivo, although some virues like A(H5N1) are thought to disproportionately stimulate host proinflammatory responses.

      • Virulence relates to the full gene constellation of influenza viruses. The severity of infections due to the 1918 pandemic virus likely related to its high levels of replication and pneumotropism.

      • In addition to overall effects on viral replication, certain gene products have been associated with increased virulence through particular mechanisms (e.g., anti-interferon effects of NS1, proinflammatory actions of PB1-F2 [although not present in A(H1N1)pdm09 virus], NA exposure of receptors to increase binding of S. pneumoniae). The presence of a polybasic amino acid cleavage site in HA allows activation of highly pathogenic avian viruses by various host proteases and fosters extrapulmonary viral dissemination, particularly to the CNS, in affected birds and certain mammalian species.

  • Host factors. In addition to contributing factors like viral inoculum size and host comorbidities, host genetic factors are likely important in the pathogenesis of severe influenza. Although specific genetic factors are as yet not defined, available epidemiologic observations indicate that they are operative in both avian A(H5N1) infections, which are rare despite ample exposures to infected birds and also which cluster in first-degree blood relatives, and in severe A(H1N1)pdm09 virus illness where the case-fatality ratio was roughly 1 in 10,000. Genome-wide studies in these conditions are currently in progress.

    • One recent study found that specific mutations in the gene encoding interferon-induced transmembrane protein 3 (IFITM3) were present more often in hospitalized patients with A(H1N1)pdm09 or seasonal influenza illness.

    • Another report of seasonal influenza cases found that fatalities with low-producing MBL2 (mannose binding lectin) genotypes had a 7-fold increased risk for invasive MRSA.

WHAT’S THE EVIDENCE for specific management and treatment recommendations?

Useful Web sites

"Seasonal Influenza (Flu)".

(Weekly updates on influenza circulation patterns, both domestic and international, and wide range of detailed information on influenza epidemiology, diagnostics, vaccines, and management for both professionals and the general public.)


(Key website for information on epidemiology and other aspects of human influenza based on surveillance through the Global Influenza Surveillance and Response System and with regular updates provided by WHO staff.)

(Daily updates on breaking news and commentary on influenza and related events.)

"Avian Influenza".

(Useful resouce for information regarding all aspects of avian influenza outbreaks.)

General references

Hayden, FG, Goldman, L, Schafer, AI. "Influenza". Goldman's Cecil Medicine. Elsevier Saunders. 2012. pp. 2095-100.

(Overview of clinical aspects of influenza infections targeted to adult medicine practitioners.)

Hayden, FG, Palese, P, Richman, DD, Whitley, RJ, Hayden, FG. "Influenza virus". Clinical Virology. American Society for Microbiology Press. 2009. pp. 943-76.

(More comprehensive review covering influenza virology, epidemiology, pathogenesis, clinical features, prevention, and treatment.)

"Proceedings of the International Conference on Options for the Control of Influenza VII, September 3-7, 2010, Hong Kong SAR, China". Influenza and Other Respiratory Viruses. vol. 5. 2011. pp. 1-446.

(Summaries of major talks on all aspects of influenza research given at the principal international meeting of influenza investigators, held every 3 years.)

Beigi, R. "Influenza during pregnancy: a cause fo serious infection in obsterics". Clinical Obstetrics and Gynecology. vol. 55. pp. 914-926.

(Overview of influenza infections in pregnancy with recommendations for prevention and treatment.)

Pandemic 2009 A(H1N1) and swine-origin viruses

"Clinical aspects of pandemic 2009 influenza A (H1N1) virus infection". N Engl J Med. vol. 362. 2010. pp. 1708-19.

(Review covering key aspects of swine-origin 2009 pandemic.)

Shieh, WJ, Blau, DM, Denison, AM. "2009 pandemic influenza A (H1N1): pathology and pathogenesis of 100 fatal cases in the United States". Am J Pathol. vol. 177. 2010. pp. 166-75.

(Autopsy data from 100 fatal pandemic 2009 cases in the United States that found viral pneumonia and diffuse alveolar damage were prominent features with bacterial coinfections in more than 25%.)

Lee, N, Chan, PK, Lui, GC. "Complications and outcomes of pandemic 2009 Influenza A (H1N1) virus infection in hospitalized adults: how do they differ from those in seasonal influenza?". J Infect Dis. vol. 203. 2011. pp. 1739-47.

(Comparison of the clinical features and outcomes of adults hospitalized with seasonal influenza or pandemic 2009 A(H1N1) illness.)

Lee, N, Chan, PK, Wong, CK. "Viral clearance and inflammatory response patterns in adults hospitalized for pandemic 2009 influenza A(H1N1) virus pneumonia". Antivir Ther. vol. 16. 2011. pp. 237-47.

(Key observational study of viral dynamics and plasma cytokine and chemokine responses in patients hospitalized with pandemic 2009 pneumonia, including the finding of generally higher and more sustained RNA viral loads despite oseltamivir in patients requiring mechanical ventilation.)

To, KK, Hung, IF, Li, IW. "Delayed clearance of viral load and marked cytokine activation in severe cases of pandemic H1N1 2009 influenza virus infection". Clin Infect Dis. vol. 50. 2010. pp. 850-9.

(Observational study comparing viral dynamics in nasopharynx, viremia, and plasma proinflammatory cytokine and chemokine levels in those with mild, hypoxemic without ARDS, or ARDS or fatal pandemic 2009 illnesses.)

Yu, H, Feng, Z, Uyeki, TM. "Risk factors for severe illness with 2009 pandemic influenza A (H1N1) virus infection in China". Clin Infect Dis. vol. 52. 2011. pp. 457-65.

(Very large observational study of patients hospitalied with influenza A(H1N1)pdm09 virus infection pneumonia in China that characterizes key risk factors.)

"Influenza A (H3N2)v transmission and guidelines—five states, 2011". MMWR Morb Mortal Wkly Rep. vol. 60. 2012. pp. 1741-4.

(Summary of epidemiologic and clinical findings on recent cases of swine-origin A(H3N2)v virus infections in five states.)

Avian A(H5N1) and A(H7N9)

"Writing Committee of the Second World Health Organization Consultation on Clinical Aspects of Human Infection with Avian Influenza A(H5N1) Virus. Update on avian influenza A (H5N1) virus infection in humans". N Engl J Med. vol. 358. 2008. pp. 261-73.

(Review covering key aspects of human infections due to avian A(H5N1) viruses.)

Chan, PKS, Lee, N, Zaman, M. "Determinants of antiviral effectiveness in influenza virus A subtype H5N1". J Infect Dis. vol. 206. 2012. pp. 1359-66.

(Retrospective analysis showing mortality reduction with oseltamivir therapy in human infections due to avian A(H5N1) viruses and factors impacting on survival.)

Aditama, TY, Samaan, G, Kusriastuti, R. "Risk factors for cluster outbreaks of avian influenza A H5N1 infection, Indonesia". Clin Infect Dis. vol. 53. 2011. pp. 1237-44.

(Analysis of risk factors for sporadic cases and clusters of A(H5N1) in Indonesia that highlights the importance of first-degree relationship to index case in risk of illness in other household members.)

Gao, R, Cao, B, Hu, Y. "Human Infection with a Novel Avian-Origin Influenza A(H7N9) Virus". N Engl J Med. 2013.

(Initial detailed description of three fatal respiratory illnesses due to novel reassortant avian A(H7N9) viruses in eastern China.)

Li, Q, Zhou, L, Zhou, M. "Preliminary Report: Epidemiology of the Avian Influenza A(H7N9) Outbreak in China". N Engl J Med. 2013.

(Descriptive epidemilogy of firt 82 laboratory-confirmed A(H7N9) cases in China. Notable for frequent history of poultry expsoure, lack of documented infections in close contacts except for two family clusters in which human-to-human transmission may have occurred, and severe illness with high mortalit in most of those affected.)

"Emergence of Avian Influenza A(H7N9) Virus Causing Severe Human Illness-China, February-April 2013". Morbidity Mortality Weekly Report. 2013.

(Update on A(H7N9) outbreak and on investigations into its origins and extent of spread.)

1918 pandemic

Murray, CJ, Lopez, AD, Chin, B, Feehan, D, Hill, KH. "Estimation of potential global pandemic influenza mortality on the basis of vital registry data from the 1918-20 pandemic: a quantitative analysis". Lancet. vol. 368. 2006. pp. 2211-8.

(Epidemiologic analyses illustrating the variation in global impact of the 1918 pandemic across countries representing different geographic and resource situations and across the states in the United States.)

Smith, GJ, Bahl, J, Vijaykrishna, D. "Dating the emergence of pandemic influenza viruses". Proc Natl Acad Sci U S A. vol. 106. 2009. pp. 11709-12.

(Virologic analyses showing that the 1918 pandemic strain likely emerged as reassortment virus that contained genes from avian, human, and possibly swine viruses.)

Sheng, ZM, Chertow, DS, Ambroggio, X. "Autopsy series of 68 cases dying before and during the 1918 influenza pandemic peak". Proc Natl Acad Sci U S A. vol. 108. 2011. pp. 16416-21.

(Autopsy series illustrating the features of influenza-associated pneumonias in the prepandemic and peak pandemic periods, including the importance of both primary viral and especially secondary bacterial processes.)

Bootsma, MC, Ferguson, NM. "The effect of public health measures on the 1918 influenza pandemic in U.S.cities". Proc Natl Acad Sci U S A. vol. 104. 2007. pp. 7588-93.

(Modelling projections of the value of various public health measures and their timing on pandemic 1918 mortality in 23 US cities, with some cities estimated to have up to 30-50% reductions in transmission rates.)

Simonsen, L, Viboud, C, Chowell, G. "The need for interdisciplinary studies of historic pandemics". Vaccine. vol. 29. 2011. pp. B1-5.

(Overview of interdisciplinary studies of 1918 and other past pandemics with links to series of more detailed epidemiologic and public health studies.)

Antivirals and other treatments

Fiore, AE, Fry, A, Shay, D, Gubareva, L, Bresee, JS, Uyeki, TM. "Antiviral agents for the treatment and chemoprophylaxis of influenza—recommendations of the Advisory Committee on Immunization Practices (ACIP)". MMWR Recomm Rep.. vol. 60. 2011. pp. 1-24.

(Updated guidance from ACIP on use of influenza antivirals for treatment and prophylaxis.)

Hernán, MA, Lipsitch, M. "Oseltamivir and risk of lower respiratory tract complications in patients with flu symptoms: a meta-analysis of eleven randomized clinical trials". Clin Infect Dis. vol. 53. 2011. pp. 277-9.

(Meta-analysis of RCT data showing that early oseltamivir therapy reduces lower respiratory tract complications leading to antibiotic use in initially uncomplicated influenza in adults.)

Hsu, J, Santesso, N, Mustafa, R. "Antivirals for treatment of influenza: a systematic review and meta-analysis of observational studies". Ann Intern Med. vol. 156. 2012. pp. 512-24.

(Rigorous analysis of the observational studies on using adamantanes and NAIs for treating influenza in variety of patient populations.)

Yu, H, Liao, Q, Yuan, Y. "Effectiveness of oseltamivir on disease progression and viral RNA shedding in patients with mild pandemic 2009 influenza A H1N1: opportunistic retrospective study of medical charts in China". BMJ. vol. 341. 2010. pp. c4779.

(Large observational study in China showing that early oseltamivir therapy reduced the likelihood of developing radiologically documented pneumonia, as well as durations of fever and viral RNA detection.)

Yang, SG, Cao, B, Liang, LR. "Antiviral therapy and outcomes of patients with pneumonia caused by influenza A pandemic (H1N1) virus". PLoS One. vol. 7. 2012. pp. e29652.

(Large observational study of patients with influenza A(H1N1)pdm09 virus-associated pneumonia that assessed responses to antiviral therapy with finding of survival benefit when treatment was initiated up to 5 days and perhaps longer after illness onset.)

Dubar, G, Azria, E, Tesnière, A. "French experience of 2009 A/H1N1v influenza in pregnant women". PLoS One. vol. 5. 2010. pp. e13112.

(Review of the French experience in A(H1N1)pdm09-infected pregnant women confirming increased risks for severe outcomes, especially in third trimester, and showing partial oseltamivir treatment benefit to 3 to 5 days after illness onset.)

Lee, N, Choi, KW, Chan, PK. "Outcomes of adults hospitalised with severe influenza". Thorax. vol. 65. 2010. pp. 510-15.

(One of several retrospective studies showing reduced mortality in hospitalized seasonal influenza patients given oseltamivir up to 4 days after illness onset.)

Sugaya, N, Shinjoh, M, Mitamura, K, Takahashi, T. "Very low pandemic influenza A (H1N1) 2009 mortality associated with early neuraminidase inhibitor treatment in Japan: analysis of 1000 hospitalized children". J Infect. vol. 63. 2011. pp. 288-94.

(Retrospective chart analysis of 1,000 hospitalized children in Japan showing that early NAI therapy, primarily oseltamivir, was associated with much lower mortality [one case] or need for mechanical ventilation [1.2%] compared with experiences in other countries.)

Ariano, RE, Sitar, DS, Zelenitsky, SA. "Enteric absorption and pharmacokinetics of oseltamivir in critically ill patients with pandemic (H1N1) influenza". CMAJ. vol. 183. 2010. pp. 357-63.

(Key article on oseltamivir pharmacokinetics in critically ill patients that found adequate absorption of oseltamivir when given by extemporaneous prepartion via nasogastric tube and no need to adjust dosages in obesity.)

Fraaij, PL, van der Vries, E, Beersma, MF. "Evaluation of the antiviral response to zanamivir administered intravenously for treatment of critically ill patients with pandemic influenza A (H1N1) infection". J Infect Dis. vol. 204. 2011. pp. 777-82.

(Case series of intravenous zanamivir use in severely ill pandemic 2009 patients.)

Hayden, FG. "Newer Influenza antivirals, biotherapeutics and combinations". Influenza and Other Respiratory Viruses. vol. 7. 2012. pp. 63-75.

(Review of effectiveness of influenza antivirals based on observations and discussion of newer antivirals and combinations in the development pipeline.)

Hung, IF, To, KK, Lee, CK. "Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection". Clin Infect Dis. vol. 52. 2011. pp. 447-56.

(Nonrandomized cohort study in which the use of convalescent plasma appeared to reduce the mortality of ICU patients with severe pandemic 2009 illness.)

Nguyen, JT, Smee, DF, Barnard, DL, Julander, JG, Gross, M, de Jong, MD, Went, GT. "Efficacy of combined therapy with amantadine, oseltamivir, and ribavirin in vivo against susceptible and amantadine-resistant influenza A viruses". PLoS One. vol. 7. 2012. pp. e31006.

(Murine model study showing that adding amantadine to other classes of antivirals improved clinical outcomes in infections caused by adamantane-resistant influenza A viruses.)

Kim, WY, Young Suh, G, Huh, JW. "Triple-combination antiviral drug for pandemic H1N1 influenza virus infection in critically ill patients on mechanical ventilation". Antimicrob Agents Chemother. vol. 55. 2011. pp. 5703-9.

(Nonrandomized observational study in Korean ICU patients suggesting a possible early mortality benefit with TCAD compared to oseltamivir monotherapy.)

Hurt, AC, Chotpitayasunondh, T, Cox, NJ. "Antiviral resistance during the 2009 influenza A H1N1 pandemic: public health, laboratory, and clinical perspectives". Lancet Infect Dis. vol. 12. 2012. pp. 240-8.

(Comprehensive review of the detection, epidemiology, virologic consequences, and clinical aspects of oseltamivir-resistance in influenza A(H1N1)pdm09 viruses.)

Hurt, AC, Hardie, K, Wilson, NJ. "Characteristics of a widespread community cluster of H275Y oseltamivir-resistant A(H1N1)pdm09 influenza in Australia". J Infect Dis. vol. 206. 2012. pp. 148-57.

(Description of recent community cluster of dually oseltamivir- and adamantane-resistant A(H1N1) 2009pdm infections in Australia.)

Brun-Buisson, C, Richard, JC, Mercat, A, Thiébaut, AC, Brochard, L. "Early corticosteroids in severe influenza A/H1N1 pneumonia and acute respiratory distress syndrome". Am J Respir Crit Care Med. vol. 183. 2011. pp. 1200-6.

(One of several observational studies of ICU patients that found not only no evidence of benefit with systemic corticosteroid in pandemic 2009-associated pneumonia or ARDS but also worse outcomes including increased mortality with earlier corticosteroid administration (<3 days of mechanical ventilation).)

Vandermeer, ML, Thomas, AR, Kamimoto, L. "Association between use of statins and mortality among patients hospitalized with laboratory-confirmed influenza virus infections: a multistate study". J Infect Dis. vol. 205. 2012. pp. 13-9.

(Recent single-season analysis from the CDC's Emerging Infections Program that reported reduced mortality in statin users hospitalized with laboratory-documented influenza compared with nonusers.)

Diagnostic testing

Ginocchio, CC, Zhang, F, Manji, R. "Evaluation of multiple test methods for the detection of the novel 2009 influenza A (H1N1) during the New York City outbreak". J Clin Virol. vol. 45. 2009. pp. 191-5.

(Comparisons of several commercial rapid antigen tests, direct immunofluorescence, rapid culture, and a commercial multiplex NAT for detecting pandemic 2009 and seasonal influenza viruses in >6,000 patients.)

Jernigan, DB, Lindstrom, SL, Johnson, JR. "Detecting 2009 pandemic influenza A (H1N1) virus infection: availability of diagnostic testing led to rapid pandemic response". Clin Infect Dis. vol. 52. 2011. pp. S36-43.

(Overview of diagnostics and new test development for pandemic 2009 A(H1N1)virus.)

Chartrand, C, Leeflang, MM, Minion, J, Brewer, T, Pai, M. "Accuracy of rapid influenza diagnostic tests: a meta-analysis". Ann Intern Med. vol. 156. 2012. pp. 500-11.

(Analysis of the sensitivity, specificity, and predictive values of first generation RAT tests for influenza.)

Tasher, D, Stein, M, Simões, EA, Shohat, T, Bromberg, M, Somekh, E. "Invasive bacterial infections in relation to influenza outbreaks, 2006-2010". Clin Infect Dis. vol. 53. 2011. pp. 1199-207.

(Epidemiologic study highlighting the importance of testing for invasive bacterial infections during epidemic influenza.)

Nonpharmaceutical interventions

Talaat, M, Afifi, S, Dueger, E. "Effects of hand hygiene campaigns on incidence of laboratory-confirmed influenza and absenteeism in schoolchildren, Cairo, Egypt". Emerg Infect Dis. vol. 17. 2011. pp. 619-25.

(Open randomized trial in Egyptian schools showing marked reductions in influenza, influenzal and gastrointestinal illnesses, and conjunctivitis with a daily hand-washing intervention.)

Cowling, BJ, Chan, KH, Fang, VJ. "Facemasks and hand hygiene to prevent influenza transmission in households: a cluster randomized trial". Ann Intern Med. vol. 151. 2009. pp. 437-46.

(This RCT in households with an influenza-positive index case found that early implementation (<36 hours after illness onset) of hand hygiene with or without masking appeared to reduce influenza in contacts.)

Loeb, M, Dafoe, N, Mahony, J. "Surgical mask vs N95 respirator for preventing influenza among health care workers: a randomized trial". JAMA. vol. 302. 2009. pp. 1865-71.

(This double-blind RCT in nurses found no important differences in frequencies of influenza infection, respiratory illness, or illness due to other respiratory viruses in those using surgical masks compared with fit-tested respirators during patient care but findings confounded by other and out-of-hospital exposures and uncertain compliance.)

MacIntyre, CR, Wang, Q, Cauchemez, S. "A cluster randomized clinical trial comparing fit-tested and non-fit-tested N95 respirators to medical masks to prevent respiratory virus infection in health care workers". Influenza Other Respi Viruses. vol. 5. 2011. pp. 170-9.

(Prospective, controlled study testing shift-long masking or respirator use in China that found approximately two-fold lower rates of clinical respiratory illness and influenza-like illness in the N95 group compared to medical masks.)

Kay, M, Zerr, DM, Englund, JA. "Shedding of pandemic (H1N1) 2009 virus among health care personnel, Seattle, Washington, USA". Emerg Infect Dis. vol. 17. 2011. pp. 639-44.

(Report on virus detection patterns in self-collected nasal washes of pandemic 2009-infected HCWs receiving oseltamivir that found the duration of infectious virus detection was 3 to 10 days after illness onset.)
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