Influenza A Virus Infection in Swine


Influenza A virus (IAV) is a common cause of respiratory disease in swine. IAV infects pig populations across the globe, but vary by geographic region. Transmission between different animal species, including pigs and people, plays a major role in the rise of new IAV strains. Control of IAV in humans and swine is mutually beneficial and vaccines play a role in effective control programs.



  • Review remarkable IAV characteristics
  • Explain the classification of IAV
  • Describe the transmission, clinical signs, lesions and diagnosis of influenza
  • Discuss control and prevention strategies centered on immunity and biosecurity


Influenza A viruses have unique characteristics

Influenza A viruses (IAVs) are a major cause of respiratory disease in pigs and people (Houser and Subbarao, 2015). IAVs have eight viral gene segments. When two different IAVs infect a single cell and gene segments get exchanged, it is called genetic reassortment (Figure 1). Reassortment contributes to viral diversity and host susceptibility and thus plays a major role in IAV evolution and infections in swine.


Figure 1: Genetic reassortment of influenza A virus (IAV). Two different IAVs infect a respiratory cell and exchange genetic material. This process is known as genetic reassortment and results in a IAV virus.


The hemagglutinin (HA or H) and neuraminidase (NA or N) proteins project from the surface of the virus as spike-like structures. The HA attaches to sialic acid-containing receptors on the host cell, allowing entry of the virus and release of viral genes into the host cell. While HA is important for attachment of the virus, the NA is important in release of progeny virus from an infected cell.


Classification of IAV genes is complicated but necessary

Subtype and genotype are key to understanding the origin and evolution of IAVs. Diagnostic assays subtype IAV based on the HA and NA, denoted by numerical classification of the HA and NA genes (e.g., H1N1). To date, there are 18 HA (H1-18) and 11 (N1-11) NA subtypes (Krammer et al., 2018). However, only three subtypes consistently persist in swine: H1N1, H1N2 and H3N2 (Vincent et al., 2020). Current swine IAV genes have origins from human seasonal or avian IAV. The year of introduction to swine and geographic region defines HA and NA genes. As a result, sequencing discerns swine adapted IAV from different geographical regions and contemporary human strains. Classifying HA and NA genes in this way informs virus evolution and the potential for antigenic drift for vaccine updates. Genotyping involves sequencing all eight viral gene segments and classifying the origin of the segment to generate a gene “constellation.” Genotyping is important for understanding new virus introduction or reassortment in a herd or pig flow.


Genetic “drift” and “shift” add diversity

IAVs are diverse and constantly changing. The high variability is the result of two processes known as antigenic drift and antigenic shift. Mutations (changes in the genome sequence) that result in small, gradual changes in the HA and NA proteins cause antigenic drift. These changes usually produce viruses that share antigenic properties. This means that antibodies against one IAV created by the host immune system likely combats a similar IAV, called cross-protection. Over time, these changes accumulate and an individual’s or population’s antibody defense mechanisms against the former HA and NA may no longer protect. A small change in an important location on the HA may also result in a loss in cross-protection. Whereas antigenic drift tends to be a gradual process, antigenic shift causes a more rapid loss in cross-protection. Antigenic shift occurs when two or more IAVs with different genes infect a single host cell and exchange gene segments. If the exchange results in a new HA and/or NA subtype or genetic lineage the outcome is antigenic shift. When shift happens, most individuals in a population have little or no immunity against the new virus.


IAV infection is common

Many animal species are susceptible

The natural reservoir for most IAVs is wild waterfowl, but IAVs commonly infect poultry and mammals, including people, pigs, dogs, and horses (Webster et al., 1992; Yoon et al., 2014). In contrast to mammals, infection in wild waterfowl occurs primarily in the intestinal tract and is usually asymptomatic (Rimondi et al., 2018).


Transmission is via direct contact and also droplets and aerosols

IAVs circulate in pigs thru the year (Walia et al., 2019), with seasonal peaks in the fall and spring. IAVs transmit by direct nose to nose contact with nasal secretions and also from coughing pigs via droplets and aerosols (Brown, 2000). IAV can also get transmitted through contact with contaminated fomites (Allerson et al). Shedding of IAV begins 1-3 days after infection, continues for 4-5 days, but can last up to 7-10 days (Brown, 2000; Janke, 2014). Infected pigs and/or caretakers are sources of IAV introduction.


Clinical signs are variable between pigs

Infections with endemic IAVs produce clinically similar respiratory disease (Karasin et al., 2000a-c, 2002; Loeffen et al., 1999; Zhou et al., 1999). Clinical signs include fever (104.9-106.7°F), anorexia, lethargy, huddling, weight loss, rapid breathing, nasal discharge and cough. All signs do not occur in all infected animals. Some pigs shed IAV without notable clinical signs. Producers occasionally report abortion due to disease effects in the sow. Multiple factors decide the clinical outcome of IAV infection. These factors include immune status (maternal antibodies, vaccination, earlier exposure, or fully susceptible), age, exposure dose, temperature, humidity, housing, and concurrent infections. Secondary bacterial infections with Actinobacillus pleuropneumoniae, Pasteurella multocida, Mycoplasma hyopneumoniae, Glaesserella (Haemophilus) parasuis, or Streptococcus suis enhance the severity of clinical disease. Recovery begins 5-7 days after onset in uncomplicated disease.


Lesions are suggestive but not confirmatory

The most consistent finding of IAVs in swine is bronchopneumonia. Affected areas are firm-to-the-touch, well-demarcated, and dark red (Figure 2). Affected areas are separated by healthy lung that is light pink and soft like a marshmallow. Concurrent bacterial infections result in more extensive lesions. Some pigs get a severe, acute form of IAV disease. In this form, the entire lung is enlarged and reddened with foam in the trachea. At the microscopic level, IAV results in the death of cells lining the conducting airways and arrival of immune cells within and surrounding these airways.


Figure 2: Typical lung damage seen in pigs infected with influenza A virus. Dark red, firm affected areas (*) separated by healthy lung (^).


Diagnosis is relatively easy

Use diagnostic testing to differentiate influenza from a variety of swine respiratory diseases. There are many diagnostic tests available for IAV that detect live virus (tissue culture), viral proteins (antigen tests), nucleic acid (real time-polymerase chain reaction (RT-PCR)), as well as virus-specific antibodies (serology). Detection of viral nucleic acid by RT-PCR is the most sensitive test available. For this reason, as well as speed and scalability, RT-PCR is the most used diagnostic test for IAV. Diagnostic laboratories commonly use two types of RT-PCR for IAV. The screening assay detects any IAV in samples. The other type identifies subtype by detecting specific H1, H3, N1, or N2 genes.


RT-PCR detects IAV genetic material in multiple respiratory or environmental sample types. Samples can be used for individual diagnosis or group monitoring. These include nasal swab, nasal wipe, oral swab, lung, trachea, lung lavage fluid, udder wipe (for suckling pig oral and nasal fluid), oral fluids, air, and environmental wipes. However, the sample type and amount of viral RNA in a sample affects the ability to subtype, sequence and isolate. In general, the higher the viral RNA and the cleaner the sample (i.e., a nasal swab is generally cleaner than oral fluids), the more likely tests that further characterize IAVs will be successful.


Immunity provides protection from disease

Protective adaptive immune responses target the HA and to a lesser extent the NA proteins. Antibodies targeting the HA head neutralize viral infection by preventing attachment of the virus to host receptors and are a major focus of vaccine development. Antibodies targeting the NA limit virus release from infected cells primarily after infection has occurred. Antibodies from sow to piglet (maternal antibodies through suckling) protect young pigs. The sow status affects the quantity of antibodies in the colostrum and milk. However, timing of suckling following birth and the number of pigs in a litter affects the quantity transferred to an individual pig. Hence, piglets may not get the same quantity or quality of passive immunity. The level of passive antibodies begins to decline about eight weeks of age.


Vaccination is a mainstay for influenza prevention in pigs. Producers commonly vaccinate sows in the breeding herd. Vaccines reduce clinical signs and associated lesions but may not completely prevent infection or spread. A poor match between the HA and NA in the vaccine and field virus compromises protection. Hemagglutination inhibition (HI) assays measure the ability of antibodies to prevent viral infection, but virus neutralization (VN) and neuraminidase inhibition (NI) assays also detect relevant antibodies. HI, NI or VN assays supply correlates of protection to assess vaccine strains for cross-reactivity against field isolates.


Treatment is supportive

There is no direct treatment for influenza approved for use in swine. Veterinarians treat influenza with supportive care, including non-steroidal anti-inflammatory drugs. Secondary bacterial infections are treated with antibiotics. Measures that reduce exposure to virus and limit other health stressors (sanitation, all-in/all-out, and isolation of new pigs) decrease disease severity.


Control of IAV in pigs and people is One Health

Human infections with swine-lineage IAVs occur with low, but regular frequency. However, person-to-person spread is not common, with the notable exception of the 2009 H1N1 pandemic IAV (Van Reeth and Vincent, 2019). It is important to emphasize that most H1 and H3 swine IAVs derive from viruses that once circulated in the human population (Nelson et al., 2015a,b). Due to the two-way transmission between people and pigs, swine act as reservoirs for older human HA and NA genes. These IAVs pose a future threat to people. Practices to reduce bidirectional transmission include: wearing dedicated clothing, boots, gloves, and masks, handwashing and showers, prohibiting indirect contact of animals through shared workforces,  vaccination and sick leave policies for caretakers. Important measures to prevent IAV transmission from pigs include enhancing biosecurity, sourcing IAV negative gilts, limiting mixing of sources and movement of pigs, vaccinating pigs, implementing proper ventilation and husbandry conditions, and prohibiting direct contact between pigs and wildlife or domestic fowl.



IAVs cause an important viral respiratory disease in swine. Diagnosis is relatively easy via RT-PCR on upper respiratory tract samples. Sequencing and analysis supply important information about the origin and evolution of the IAV strain. Although H1N1, H1N2, and H3N2 IAV are endemic in pigs worldwide, many hosts share IAV. People often transmit strains to pigs and to a lesser extent in the reverse. Virus spillover between species and migration of regional strains increase genetic diversity in swine. Treatment is supportive and may include non-steroidal anti-inflammatory drugs. Vaccination is often performed in the breeding herd and is paramount to disease prevention. Matching the HA and NA between vaccine and field strains is critical. In addition to vaccination, use of multiple precautions prevents interspecies transmission or spread of endemic swine IAV among herds.


References and Citations

Allerson MW, Cardona CJ, Torremorell M. Indirect Transmission of Influenza A Virus between Pig Populations under Two Different Biosecurity Settings. PLoS One. 2013 Jun 21;8(6):e67293. doi: 10.1371/journal.pone.0067293. PMID: 23805306; PMCID: PMC3689715.


Brown, I. H. 2000. The epidemiology and evolution of influenza viruses in pigs. Vet. Microbiol. 74:29-46.


Houser, K., and K. Subbarao. 2015. Influenza vaccines: challenges and solutions. Cell Host Microbe. 17:295-300.


Janke, B. H. 2014. Influenza A Virus Infections in Swine: Pathogenesis and Diagnosis. Vet. Pathol. 51:410-426.


Karasin A. I., G. A. Anderson, C. W. Olsen. 2000a. Genetic characterization of an H1N2 influenza virus isolated from a pig in Indiana. J. Clin. Microbiol. 38:2453-2456.


Karasin A. I., I. H. Brown, S. Carman, C. W. Olsen. 2000b. Isolation and characterization of H4N6 avian influenza viruses from pigs with pneumonia in Canada. J. Virol. 74:9322-9327.


Karasin A. I., M. M. Schutten, L. A. Cooper, C. B. Smith, K. Subbarao, G. A. Anderson, S. Carman, C. W. Olsen. 2000c. Genetic characterization of H3N2 influenza viruses isolated from pigs in North America, 1977-1999: evidence for wholly human and reassortant virus genotypes. Virus Res. 68:71-85.


Karasin A. I., J. G. Landgraf, S. L. Swenson, G. Erickson, S. M. Goyal, M. Woodruff, G. Scherba, G. A. Anderson, C. W. Olsen. 2002. Genetic characterization of H1N2 influenza A viruses isolated from pigs throughout the United States. J. Clin. Microbiol. 40:1073-1079.


Krammer, F., G. J. D. Smith, R.A.M. Fouchier, M. Peiris, K. Kedzierska, P. C. Doherty, P. Palese, M. L. Shaw, J. Treanor, R. G. Webster, A. García-Sastre. 2018. Influenza. Nat. Rev. Dis. Primers. 4:3.


Loeffen W. L. A., E. M. Kamp, N. Stockhofe-Zurwieden, A. P. K. M. I. van Nieuwstadt, J. H. Bongers, W. A. Hunneman, A. R. W. Elbers, J. Baars, T. Nell, F. G. van Zijderveld. 1999. Survey of infectious agents involved in acute respiratory disease in finishing pigs. Vet. Rec. 145:123-129.


Nelson M., M. R. Culhane, A. Rovira, M. Torremorell, P. Guerrero, J. Norambuena. 2015a. Novel Human-like Influenza A Viruses Circulate in Swine in Mexico and Chile. PLoS Curr 7.


Nelson M. I., R. Schaefer, D. Gava, M. E. Cantao, J. R. Ciacci-Zanella. 2015b. Influenza A Viruses of Human Origin in Swine, Brazil. Emerg. Infect. Dis. 21:1339-1347.


Rimondi, A., A. S. Gonzalez-Reiche, V. S. Olivera, J. Decarre, G. J. Castresana, M. Romano, M. I. Nelson, H. van Bakel, A. J. Pereda, L. Ferreri, G. Geiger, and D. R. Perez. 2018. Evidence of a fixed internal gene constellation in influenza A viruses isolated from wild birds in Argentina (2006-2016). Emerg. Microbes Infect. 7:194.


Van Reeth K. and A. L. Vincent. 2019. Influenza viruses. In: Diseases of Swine. J. J. Zimmerman, L. A. Karriker, A. Ramirez, K. J. Schwartz, G. W. Stevenson, J. Zhang. Wiley-Blackwell, Hoboken, NJ. p. 576-593.


Vincent, A. L., T. K. Anderson, K. M. Lager. 2020. A Brief Introduction to Influenza A Virus in Swine. Methods Mol. Biol. 2123:249-271.


Walia, R. R., T. K. Anderson, A. L. Vincent. 2019. Regional patterns of genetic diversity in swine influenza A viruses in the United States from 2010 to 2016. Influenza Other Respi Viruses. 13:262–273.


Webster R. G., W.J. Bean, O.T. Gorman, T.M. Chambers, Y. Kawaoka. 1992. Evaluation of ecology of influenza A virus. Microbiol. Rev. 56:152-179.


Zhou N. N., D. A. Senne, J.S. Landgraf, S. L. Swenson, G. Erickson, K. Rossow, L. Liu, K-J Yoon, S. Krauss, R. G. Webster. 1999. Genetic reassortment of avian, swine, and human influenza A viruses in American pigs. J. Virol. 73:8851-8856.




Reference to products in this publication is not intended to be an endorsement to the exclusion of others which may be similar. Persons using such products assume responsibility for their use in accordance with current directions of the manufacturer. The information represented herein is believed to be accurate but is in no way guaranteed. The authors, reviewers, and publishers assume no liability in connection with any use for the products discussed and make no warranty, expressed or implied, in that respect, nor can it be assumed that all safety measures are indicated herein or that additional measures may be required. The user therefore, must assume full responsibility, both as to persons and as to property, for the use of these materials including any which might be covered by patent. This material may be available in alternative formats.