Chapter 81 : Influenza Viruses

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This chapter discusses about Influenza viruses that cause annual epidemics in areas with temperate climates, while in tropical climates seasonality is less apparent and influenza viruses can be isolated throughout the year. Influenza viruses are transmitted from person to person primarily via droplets generated by sneezing, coughing, and speaking. Direct or indirect (fomite) contact with contaminated secretions and small-particle aerosols are other potential routes of transmission that have been noted. The relative importance of different routes has not been determined for influenza viruses. Influenza viruses infect the respiratory epithelium and can be found in respiratory secretions of all types. A number of transport media are suitable for influenza viruses, including veal infusion broth, Hanks balanced salt solution, tryptose phosphate broth, sucrose phosphate buffer, and commercially available cell culture medium. Molecular methods are increasingly being used for both the detection and the characterization of influenza viruses. The most commonly used molecular method is reverse transcription-PCR (RT-PCR). The initial step is to identify the isolate as an influenza virus and to distinguish it from other respiratory viruses that have the ability to agglutinate or adsorb red blood cells. Cell culture assays do not reliably identify antiviral susceptibility to the NA inhibitors (NAIs) zanamivir and oseltamivir. Influenza viruses isolated in national and global surveillance systems are characterized antigenically and genetically to identify variants.

Citation: Atmar R, Lindstrom S. 2011. Influenza Viruses, p 1333-1346. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch81
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Image of FIGURE 1

Influenza virus-infected MDCK cells. (A) Cytopathic changes. (B) Hemadsorption with guinea pig red blood cells. Red blood cells adsorb to both infected cells (black arrows) and the plastic surface, previously occupied by infected cells (white arrowheads).

Citation: Atmar R, Lindstrom S. 2011. Influenza Viruses, p 1333-1346. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch81
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Commercially available kits for detection of influenza A or B viruses by FA staining

Abbreviations: IFA, indirect fluorescent antibody; DFA, direct fluorescent antibody; NA, nasal aspirate; NPA, nasopharyngeal aspirate; NPS, nasopharyngeal swab; NW, nasal wash fluid; TS, throat swab; N/A, not applicable; RSV, respiratory syncytial virus; P1, P2, and P3, parainfluenza virus types 1, 2, and 3, respectively.

Citation: Atmar R, Lindstrom S. 2011. Influenza Viruses, p 1333-1346. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch81
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Table 2

Commercially available kits for rapid (≤30-min) detection of influenza A or B viruses

Abbreviations: EIA, enzyme immunoassay; BAL, bronchoalveolar lavage fluid; NA, nasal aspirate; NPS, nasopharyngeal swab; NS, nasal swab; NW, nasal wash fluid; TS, throat swab.

Test characteristics were compiled from published literature.

CLIA waived laboratory assays employ methodologies that are so simple and accurate as to render the likelihood of erroneous results negligible. CLIA moderate complexity assays require some knowledge, training, reagent preparation, processing, proficiency, ability to troubleshoot, or interpretation and judgment in the performance of the test.

Citation: Atmar R, Lindstrom S. 2011. Influenza Viruses, p 1333-1346. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch81
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Table 3

Commercially available and selected other molecular detection assays for influenza viruses

Not all available test kits may be listed here. Abbreviations: BAL, bronchoalveolar lavage fluid; BW, bronchial wash; NPA, nasopharyngeal aspirate; NPS, nasopharyngeal swab; NS, nasal swab; NW, nasal wash fluid; TA, tracheal aspirate; TS, throat swab; RSV, respiratory syncytial virus; P1, P2, P3, and P4, parainfluenza virus types 1, 2, 3, and 4, respectively; hMPV, human metapneumovirus; HRV, human rhinovirus; Ent, enterovirus; Ad, adenovirus; Boca, bocavirus; OC43, 229E, NL63, and HKU1, human coronavirus variants.

Availability limited to U.S. public health laboratories.

Additional virus strains identified in the RV15 panel.

Citation: Atmar R, Lindstrom S. 2011. Influenza Viruses, p 1333-1346. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch81
Generic image for table
Table 4

Methods to identify and characterize influenza virus isolates

Citation: Atmar R, Lindstrom S. 2011. Influenza Viruses, p 1333-1346. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch81

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