Development and Evaluation of New Real-Time RT-PCR Assays for Identifying the Influenza A Virus Cluster IV H3N2 Variant

From 2005 to July 6, 2018, a total of 435 swine-origin influenza A H3N2 variant virus (H3N2v) infections in humans were reported in the USA. The largest H3N2v outbreak in the USA occurred in 2011–2012. This virus obtained the HA gene from the human seasonal H3N2 influenza A viruses (seasonal H3N2) v...

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Published inJapanese Journal of Infectious Diseases Vol. 72; no. 2; pp. 127 - 129
Main Authors Saito, Shinji, Nakauchi, Mina, Takayama, Ikuyo, Nagata, Shiho, Odagiri, Takato, Kageyama, Tsutomu
Format Journal Article
LanguageEnglish
Published Japan National Institute of Infectious Diseases, Japanese Journal of Infectious Diseases Editorial Committee 31.03.2019
Japan Science and Technology Agency
Subjects
Assaying
cluster IV H3N2v
Clusters
detection
Health risks
Influenza
Influenza A
Outbreaks
Polymerase chain reaction
Public health
Real time
real-time RT-PCR
seasonal H3N2
Swine
Viruses
United States > US
influenza
seasonal H3N2
detection
cluster IV H3N2v
real-time RT-PCR
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Abstract From 2005 to July 6, 2018, a total of 435 swine-origin influenza A H3N2 variant virus (H3N2v) infections in humans were reported in the USA. The largest H3N2v outbreak in the USA occurred in 2011–2012. This virus obtained the HA gene from the human seasonal H3N2 influenza A viruses (seasonal H3N2) via human-to-swine transmission in the mid-1990s and was classified as Cluster IV H3N2v. For early detection of public health threats associated with Cluster IV H3N2v distinct from seasonal H3N2, we developed highly specific and sensitive one-step real-time RT-PCR assays directly targeting the HA genes of Cluster IV H3N2v and seasonal H3N2. These assays are useful for the systematic surveillance and identification of Cluster IV H3N2v.
AbstractList From 2005 to July 6, 2018, a total of 435 swine-origin influenza A H3N2 variant virus (H3N2v) infections in humans were reported in the USA. The largest H3N2v outbreak in the USA occurred in 2011-2012. This virus obtained the HA gene from the human seasonal H3N2 influenza A viruses (seasonal H3N2) via human-to-swine transmission in the mid-1990s and was classified as Cluster IV H3N2v. For early detection of public health threats associated with Cluster IV H3N2v distinct from seasonal H3N2, we developed highly specific and sensitive one-step real-time RT-PCR assays directly targeting the HA genes of Cluster IV H3N2v and seasonal H3N2. These assays are useful for the systematic surveillance and identification of Cluster IV H3N2v.From 2005 to July 6, 2018, a total of 435 swine-origin influenza A H3N2 variant virus (H3N2v) infections in humans were reported in the USA. The largest H3N2v outbreak in the USA occurred in 2011-2012. This virus obtained the HA gene from the human seasonal H3N2 influenza A viruses (seasonal H3N2) via human-to-swine transmission in the mid-1990s and was classified as Cluster IV H3N2v. For early detection of public health threats associated with Cluster IV H3N2v distinct from seasonal H3N2, we developed highly specific and sensitive one-step real-time RT-PCR assays directly targeting the HA genes of Cluster IV H3N2v and seasonal H3N2. These assays are useful for the systematic surveillance and identification of Cluster IV H3N2v.
From 2005 to July 6, 2018, a total of 435 swine-origin influenza A H3N2 variant virus (H3N2v) infections in humans were reported in the USA. The largest H3N2v outbreak in the USA occurred in 2011–2012. This virus obtained the HA gene from the human seasonal H3N2 influenza A viruses (seasonal H3N2) via human-to-swine transmission in the mid-1990s and was classified as Cluster IV H3N2v. For early detection of public health threats associated with Cluster IV H3N2v distinct from seasonal H3N2, we developed highly specific and sensitive one-step real-time RT-PCR assays directly targeting the HA genes of Cluster IV H3N2v and seasonal H3N2. These assays are useful for the systematic surveillance and identification of Cluster IV H3N2v.
Author Saito, Shinji
Odagiri, Takato
Nagata, Shiho
Nakauchi, Mina
Kageyama, Tsutomu
Takayama, Ikuyo
Author_xml – sequence: 1
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  fullname: Takayama, Ikuyo
  organization: Influenza Virus Research Center, National Institute of Infectious Diseases
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  fullname: Odagiri, Takato
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  fullname: Kageyama, Tsutomu
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10.7883/yoken.JJID.2014.136
10.1093/cid/cit649
10.1016/j.jviromet.2010.10.018
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7. Diaz A, Marthaler D, Corzo C, et al. Multiple Genome Constellations of Similar and Distinct Influenza A Viruses Co-Circulate in Pigs During Epidemic Events. Sci Rep. 2017;7:11886.
14. Nakauchi M, Takayama I, Takahashi H, et al. Real-time RT-PCR assays for discriminating influenza B virus Yamagata and Victoria lineages. J Virol Methods. 2014;205:110-5.
8. Kyriakis CS, Zhang M, Wolf S, et al. Molecular epidemiology of swine influenza A viruses in the Southeastern United States, highlights regional differences in circulating strains. Vet Microbiol. 2017;211:174-9.
4. Jhung MA, Epperson S, Biggerstaff M, et al. Outbreak of variant influenza A(H3N2) virus in the United States. Clin Infect Dis. 2013;57:1703-12.
11. Nakauchi M, Yasui Y, Miyoshi T, et al. One-step real-time reverse transcription-PCR assays for detecting and subtyping pandemic influenza A/H1N1 2009, seasonal influenza A/H1N1, and seasonal influenza A/H3N2 viruses. J Virol Methods. 2011;171:156-62.
10. United States Department of Agriculture. Influenza A Virus in Swine Surveillance. Availabe at <https://www.aphis.usda.gov/animal_health/animal_dis_spec/swine/downloads/fy2018quarter1swinereport.pdf>. Accessed June 26, 2018.
13. Saito S, Takayama I, Nakauchi M, et al. Development and evaluation of a new real-time RT-PCR assay for detecting the latest H9N2 influenza viruses capable of causing human infections. Microbiol Immunol. Epub 2019 Jan 1. DOI: 10.1111/1348-0421.12666.
12. Takayama I, Nakauchi M, Takahashi H, et al. Development of Real-time Reverse Transcription Loop-Mediated Isothermal Amplification Assay with Quenching Primer for Influenza Virus and Respiratory Syncytial Virus. J Virol Methods. https://doi.org/10.1016/j.jviromet.2019.02.010.
2. Lindstrom S, Garten R, Balish A, et al. Human infections with novel reassortant influenza A(H3N2)v viruses, United States, 2011. Emerg Infect Dis. 2012;18:834-7.
9. Walia RR, Anderson TK, Vincent AL. Regional patterns of genetic diversity in swine influenza A viruses in the United States from 2010 to 2016. Influenza Other Respir Viruses. 2018.
6. Bowman AS, Walia RR, Nolting JM, et al. Influenza A(H3N2) Virus in Swine at Agricultural Fairs and Transmission to Humans, Michigan and Ohio, USA, 2016. Emerg Infect Dis. 2017;23:1551-5.
1. Centers for Disease Control and Prevention. First Variant Virus Infection of 2018 Linked to Pig Exposure at an Agricultural Fair in Indiana.Availabe at <https://www.cdc.gov/flu/news/variant-virus-2018.htm>. Accessed June 26, 2018.
3. Bowman AS, Nelson SW, Page SL, et al. Swine-to-human transmission of influenza A(H3N2) virus at agricultural fairs, Ohio, USA, 2012. Emerg Infect Dis. 2014;20:1472-80.
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References_xml – reference: 6. Bowman AS, Walia RR, Nolting JM, et al. Influenza A(H3N2) Virus in Swine at Agricultural Fairs and Transmission to Humans, Michigan and Ohio, USA, 2016. Emerg Infect Dis. 2017;23:1551-5.
– reference: 7. Diaz A, Marthaler D, Corzo C, et al. Multiple Genome Constellations of Similar and Distinct Influenza A Viruses Co-Circulate in Pigs During Epidemic Events. Sci Rep. 2017;7:11886.
– reference: 11. Nakauchi M, Yasui Y, Miyoshi T, et al. One-step real-time reverse transcription-PCR assays for detecting and subtyping pandemic influenza A/H1N1 2009, seasonal influenza A/H1N1, and seasonal influenza A/H3N2 viruses. J Virol Methods. 2011;171:156-62.
– reference: 3. Bowman AS, Nelson SW, Page SL, et al. Swine-to-human transmission of influenza A(H3N2) virus at agricultural fairs, Ohio, USA, 2012. Emerg Infect Dis. 2014;20:1472-80.
– reference: 5. Schicker RS, Rossow J, Eckel S, et al. Outbreak of Influenza A(H3N2) Variant Virus Infections Among Persons Attending Agricultural Fairs Housing Infected Swine - Michigan and Ohio, July–August 2016. MMWR Morb Mortal Wkly Rep. 2016;65:1157-60.
– reference: 12. Takayama I, Nakauchi M, Takahashi H, et al. Development of Real-time Reverse Transcription Loop-Mediated Isothermal Amplification Assay with Quenching Primer for Influenza Virus and Respiratory Syncytial Virus. J Virol Methods. https://doi.org/10.1016/j.jviromet.2019.02.010.
– reference: 2. Lindstrom S, Garten R, Balish A, et al. Human infections with novel reassortant influenza A(H3N2)v viruses, United States, 2011. Emerg Infect Dis. 2012;18:834-7.
– reference: 14. Nakauchi M, Takayama I, Takahashi H, et al. Real-time RT-PCR assays for discriminating influenza B virus Yamagata and Victoria lineages. J Virol Methods. 2014;205:110-5.
– reference: 8. Kyriakis CS, Zhang M, Wolf S, et al. Molecular epidemiology of swine influenza A viruses in the Southeastern United States, highlights regional differences in circulating strains. Vet Microbiol. 2017;211:174-9.
– reference: 1. Centers for Disease Control and Prevention. First Variant Virus Infection of 2018 Linked to Pig Exposure at an Agricultural Fair in Indiana.Availabe at <https://www.cdc.gov/flu/news/variant-virus-2018.htm>. Accessed June 26, 2018.
– reference: 9. Walia RR, Anderson TK, Vincent AL. Regional patterns of genetic diversity in swine influenza A viruses in the United States from 2010 to 2016. Influenza Other Respir Viruses. 2018.
– reference: 4. Jhung MA, Epperson S, Biggerstaff M, et al. Outbreak of variant influenza A(H3N2) virus in the United States. Clin Infect Dis. 2013;57:1703-12.
– reference: 13. Saito S, Takayama I, Nakauchi M, et al. Development and evaluation of a new real-time RT-PCR assay for detecting the latest H9N2 influenza viruses capable of causing human infections. Microbiol Immunol. Epub 2019 Jan 1. DOI: 10.1111/1348-0421.12666.
– reference: 15. Takayama I, Takahashi H, Nakauchi M, et al. Development of a diagnostic system for novel influenza A(H7N9) virus using a real-time RT-PCR assay in Japan. Jpn J Infect Dis. 2015;68:113-8.
– reference: 10. United States Department of Agriculture. Influenza A Virus in Swine Surveillance. Availabe at <https://www.aphis.usda.gov/animal_health/animal_dis_spec/swine/downloads/fy2018quarter1swinereport.pdf>. Accessed June 26, 2018.
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SubjectTerms Assaying
cluster IV H3N2v
Clusters
detection
Health risks
Influenza
Influenza A
Outbreaks
Polymerase chain reaction
Public health
Real time
real-time RT-PCR
seasonal H3N2
Swine
Viruses
Title Development and Evaluation of New Real-Time RT-PCR Assays for Identifying the Influenza A Virus Cluster IV H3N2 Variant
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