Improved Subtyping of Avian Influenza Viruses Using an RT-qPCR-Based Low Density Array: ‘Riems Influenza a Typing Array’, Version 2 (RITA-2)
Avian influenza virus (AIV) variants emerge frequently, which challenges rapid diagnosis. Appropriate diagnosis reaching the sub- and pathotype level is the basis of combatting notifiable AIV infections. Real-time RT-PCR (RT-qPCR) has become a standard diagnostic tool. Here, a total of 24 arrayed RT...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-02-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/2/415 |
| _version_ | 1797476012336873472 |
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| author | Kareem E. Hassan Ann Kathrin Ahrens Ahmed Ali Magdy F. El-Kady Hafez M. Hafez Thomas C. Mettenleiter Martin Beer Timm Harder |
| author_facet | Kareem E. Hassan Ann Kathrin Ahrens Ahmed Ali Magdy F. El-Kady Hafez M. Hafez Thomas C. Mettenleiter Martin Beer Timm Harder |
| author_sort | Kareem E. Hassan |
| collection | DOAJ |
| description | Avian influenza virus (AIV) variants emerge frequently, which challenges rapid diagnosis. Appropriate diagnosis reaching the sub- and pathotype level is the basis of combatting notifiable AIV infections. Real-time RT-PCR (RT-qPCR) has become a standard diagnostic tool. Here, a total of 24 arrayed RT-qPCRs is introduced for full subtyping of 16 hemagglutinin and nine neuraminidase subtypes of AIV. This array, designated Riems Influenza A Typing Array version 2 (RITA-2), represents an updated and economized version of the RITA-1 array previously published by Hoffmann et al. RITA-2 provides improved integration of assays (24 instead of 32 parallel reactions) and reduced assay volume (12.5 µL). The technique also adds RT-qPCRs to detect Newcastle Disease (NDV) and Infectious Bronchitis viruses (IBV). In addition, it maximizes inclusivity (all sequences within one subtype) and exclusivity (no intersubtypic cross-reactions) as shown in validation runs using a panel of 428 AIV reference isolates, 15 reference samples each of NDV and IBV, and 122 clinical samples. The open format of RITA-2 is particularly tailored to subtyping influenza A virus of avian hosts and Eurasian geographic origin. Decoupling and re-arranging selected RT-qPCRs to detect specific AIV variants causing epizootic outbreaks with a temporal and/or geographic restriction is possible. |
| first_indexed | 2024-03-09T20:51:51Z |
| format | Article |
| id | doaj.art-b55646a085c743d8a631afc9c5c2b4ea |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T20:51:51Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-b55646a085c743d8a631afc9c5c2b4ea2023-11-23T22:32:31ZengMDPI AGViruses1999-49152022-02-0114241510.3390/v14020415Improved Subtyping of Avian Influenza Viruses Using an RT-qPCR-Based Low Density Array: ‘Riems Influenza a Typing Array’, Version 2 (RITA-2)Kareem E. Hassan0Ann Kathrin Ahrens1Ahmed Ali2Magdy F. El-Kady3Hafez M. Hafez4Thomas C. Mettenleiter5Martin Beer6Timm Harder7Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, GermanyInstitute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, GermanyDepartment of Poultry Diseases, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, EgyptDepartment of Poultry Diseases, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, EgyptInstitute of Poultry Diseases, Free University Berlin, 14163 Berlin, GermanyFriedrich-Loeffler-Institute, 17493 Greifswald-Insel Riems, GermanyInstitute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, GermanyInstitute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, GermanyAvian influenza virus (AIV) variants emerge frequently, which challenges rapid diagnosis. Appropriate diagnosis reaching the sub- and pathotype level is the basis of combatting notifiable AIV infections. Real-time RT-PCR (RT-qPCR) has become a standard diagnostic tool. Here, a total of 24 arrayed RT-qPCRs is introduced for full subtyping of 16 hemagglutinin and nine neuraminidase subtypes of AIV. This array, designated Riems Influenza A Typing Array version 2 (RITA-2), represents an updated and economized version of the RITA-1 array previously published by Hoffmann et al. RITA-2 provides improved integration of assays (24 instead of 32 parallel reactions) and reduced assay volume (12.5 µL). The technique also adds RT-qPCRs to detect Newcastle Disease (NDV) and Infectious Bronchitis viruses (IBV). In addition, it maximizes inclusivity (all sequences within one subtype) and exclusivity (no intersubtypic cross-reactions) as shown in validation runs using a panel of 428 AIV reference isolates, 15 reference samples each of NDV and IBV, and 122 clinical samples. The open format of RITA-2 is particularly tailored to subtyping influenza A virus of avian hosts and Eurasian geographic origin. Decoupling and re-arranging selected RT-qPCRs to detect specific AIV variants causing epizootic outbreaks with a temporal and/or geographic restriction is possible.https://www.mdpi.com/1999-4915/14/2/415avian influenzadiagnosisreal-time RT-PCRNewcastle disease virusinfectious bronchitis virus |
| spellingShingle | Kareem E. Hassan Ann Kathrin Ahrens Ahmed Ali Magdy F. El-Kady Hafez M. Hafez Thomas C. Mettenleiter Martin Beer Timm Harder Improved Subtyping of Avian Influenza Viruses Using an RT-qPCR-Based Low Density Array: ‘Riems Influenza a Typing Array’, Version 2 (RITA-2) Viruses avian influenza diagnosis real-time RT-PCR Newcastle disease virus infectious bronchitis virus |
| title | Improved Subtyping of Avian Influenza Viruses Using an RT-qPCR-Based Low Density Array: ‘Riems Influenza a Typing Array’, Version 2 (RITA-2) |
| title_full | Improved Subtyping of Avian Influenza Viruses Using an RT-qPCR-Based Low Density Array: ‘Riems Influenza a Typing Array’, Version 2 (RITA-2) |
| title_fullStr | Improved Subtyping of Avian Influenza Viruses Using an RT-qPCR-Based Low Density Array: ‘Riems Influenza a Typing Array’, Version 2 (RITA-2) |
| title_full_unstemmed | Improved Subtyping of Avian Influenza Viruses Using an RT-qPCR-Based Low Density Array: ‘Riems Influenza a Typing Array’, Version 2 (RITA-2) |
| title_short | Improved Subtyping of Avian Influenza Viruses Using an RT-qPCR-Based Low Density Array: ‘Riems Influenza a Typing Array’, Version 2 (RITA-2) |
| title_sort | improved subtyping of avian influenza viruses using an rt qpcr based low density array riems influenza a typing array version 2 rita 2 |
| topic | avian influenza diagnosis real-time RT-PCR Newcastle disease virus infectious bronchitis virus |
| url | https://www.mdpi.com/1999-4915/14/2/415 |
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