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Editor, Senior Moderator
J Vet Sci. 2019 Sep;20(5):e56. doi: 10.4142/jvs.2019.20.e56. [h=1]The difference of detection rate of avian influenza virus in the wild bird surveillance using various methods.[/h]
Kim GS[SUP]1[/SUP], Kim TS[SUP]1[/SUP], Son JS[SUP]1[/SUP], Lai VD[SUP]1[/SUP], Park JE[SUP]2[/SUP], Wang SJ[SUP]2[/SUP], Jheong WH[SUP]2[/SUP], Mo IP[SUP]3[/SUP].
[h=3]Author information[/h] 1 Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea. 2 Environmental Health Research Division, National Institute of Environmental Research, Incheon 22689, Korea. 3 Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea. moip@cbu.ac.kr.
[h=3]Abstract[/h] Korea is located within the East Asian-Australian flyway of wild migratory birds during the fall and winter seasons. Consequently, the likelihood of introduction of numerous subtypes and pathotypes of the Avian influenza (AI) virus to Korea has been thought to be very high. In the current study, we surveyed wild bird feces for the presence of AI virus that had been introduced to Korea between September 2017 and February 2018. To identify and characterize the AI virus, we employed commonly used methods, namely, virus isolation (VI) via egg inoculation, real-time reverse transcription-polymerase chain reaction (rRT-PCR), conventional RT-PCR (cRT-PCR) and a newly developed next generation sequencing (NGS) approach. In this study, 124 out of 11,145 fresh samples of wild migratory birds tested were rRT-PCR positive; only 52.0% of VI positive samples were determined as positive by rRT-PCR from fecal supernatant. Fifty AI virus specimens were isolated from fresh fecal samples and typed. The cRT-PCR subtyping results mostly coincided with the NGS results, although NGS detected the presence of 11 HA genes and four NA genes that were not detected by cRT-PCR. NGS analysis confirmed that 12% of the identified viruses were mixed-subtypes which were not detected by cRT-PCR. Prevention of the occurrence of AI virus requires a workflow for rapid and accurate virus detection and verification. However, conventional methods of detection have some limitations. Therefore, different methods should be combined for optimal surveillance, and further studies are needed in aspect of the introduction and application of new methods such as NGS.
? 2019 The Korean Society of Veterinary Science.
[h=4]KEYWORDS:[/h] Avian influenza; Korea; conventional method; next generation sequencing; wild bird
PMID: 31565899 DOI: 10.4142/jvs.2019.20.e56
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Kim GS[SUP]1[/SUP], Kim TS[SUP]1[/SUP], Son JS[SUP]1[/SUP], Lai VD[SUP]1[/SUP], Park JE[SUP]2[/SUP], Wang SJ[SUP]2[/SUP], Jheong WH[SUP]2[/SUP], Mo IP[SUP]3[/SUP].
[h=3]Author information[/h] 1 Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea. 2 Environmental Health Research Division, National Institute of Environmental Research, Incheon 22689, Korea. 3 Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea. moip@cbu.ac.kr.
[h=3]Abstract[/h] Korea is located within the East Asian-Australian flyway of wild migratory birds during the fall and winter seasons. Consequently, the likelihood of introduction of numerous subtypes and pathotypes of the Avian influenza (AI) virus to Korea has been thought to be very high. In the current study, we surveyed wild bird feces for the presence of AI virus that had been introduced to Korea between September 2017 and February 2018. To identify and characterize the AI virus, we employed commonly used methods, namely, virus isolation (VI) via egg inoculation, real-time reverse transcription-polymerase chain reaction (rRT-PCR), conventional RT-PCR (cRT-PCR) and a newly developed next generation sequencing (NGS) approach. In this study, 124 out of 11,145 fresh samples of wild migratory birds tested were rRT-PCR positive; only 52.0% of VI positive samples were determined as positive by rRT-PCR from fecal supernatant. Fifty AI virus specimens were isolated from fresh fecal samples and typed. The cRT-PCR subtyping results mostly coincided with the NGS results, although NGS detected the presence of 11 HA genes and four NA genes that were not detected by cRT-PCR. NGS analysis confirmed that 12% of the identified viruses were mixed-subtypes which were not detected by cRT-PCR. Prevention of the occurrence of AI virus requires a workflow for rapid and accurate virus detection and verification. However, conventional methods of detection have some limitations. Therefore, different methods should be combined for optimal surveillance, and further studies are needed in aspect of the introduction and application of new methods such as NGS.
? 2019 The Korean Society of Veterinary Science.
[h=4]KEYWORDS:[/h] Avian influenza; Korea; conventional method; next generation sequencing; wild bird
PMID: 31565899 DOI: 10.4142/jvs.2019.20.e56
Free full text