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Jonas M, Sahesti A, Murwijati T, Lestariningsih CL, Irine I, Ayesda CS, Prihartini W, Mahardika GN. Identification of avian influenza virus subtype H9N2 in chicken farms in Indonesia. Prev Vet Med 2018; 159:99-105. [PMID: 30314797 DOI: 10.1016/j.prevetmed.2018.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 02/11/2018] [Accepted: 09/04/2018] [Indexed: 11/25/2022]
Abstract
Avian influenza virus subtype H9N2 (AIV-H9N2) has become established in domestic poultry in Asia and Africa. AIV-H9N2 has not been reported previously in Indonesia. Here we describe the presence of AIV-H9N2 in chicken farms in Indonesia. Ninety-nine cases were observed in various provinces in Indonesia. Clinical signs, pathologic lesions and egg production were recorded. Confirmation was made using virus isolation, reverse transcriptase PCR (RT-PCR), and sequencing. To construct hemaglutinin (HA) phylogeny, the secondary data of Eurasian lineages were downloaded from GenBank. For neuraminidase, five sequences with the highest similarities with every sequence found in this study were downloaded. Phylogeny was inferred using Neighbor-Joining method in MEGA6 package. Forty-nine AIV-H9N2-positive cases were observed, of which 35 were tested positive for AIV-H9N2 only. The age of the infected chickens was 43.17 ± 16.56 weeks, and their egg production was 35.85 ± 17.80% lower than before outbreak. BLAST search revealed that the nucleotide sequence of the HA-encoding gene identified in this study shared 98% sequence identity with that of A/Muscovy duck/Vietnam/LBM719/2014(H9N2), while its neuraminidase-encoding gene sequences shared 94%, 98%, and 100% identities with three different influenza viruses. The phylogeny shows that the HA of AIV-H9N2 found in this study forms distinct cluster with some Vietnam and China's sequence data. The NA sequence data form three distinct clusters. We conclude that AIV-H9N2 is widespread in many provinces in Indonesia. To lessen economic losses to the poultry industry, flock biosecurity and vaccination against this virus subtype should be implemented rapidly. Thorough and rigid AIV surveillance is paramount to prevent further veterinary and public health consequences of the circulation of this virus in Indonesia.
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Affiliation(s)
- Melina Jonas
- PT Medion Farma Jaya, Jl. Babakan Ciparay #282, Bandung, Indonesia
| | - Aprilla Sahesti
- PT Medion Farma Jaya, Jl. Babakan Ciparay #282, Bandung, Indonesia
| | | | | | - Ine Irine
- PT Medion Farma Jaya, Jl. Babakan Ciparay #282, Bandung, Indonesia
| | | | - Wahyu Prihartini
- PT Medion Farma Jaya, Jl. Babakan Ciparay #282, Bandung, Indonesia
| | - Gusti Ngurah Mahardika
- Faculty of Veterinary Medicine Udayana University, Jl. PB Sudirman, 80225, Denpasar, Bali, Indonesia.
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Wang C, Wang Q, Hu J, Sun H, Pu J, Liu J, Sun Y. A Multiplex RT-PCR Assay for Detection and Differentiation of Avian-Origin Canine H3N2, Equine-Origin H3N8, Human-Origin H3N2, and H1N1/2009 Canine Influenza Viruses. PLoS One 2017; 12:e0170374. [PMID: 28107507 PMCID: PMC5249048 DOI: 10.1371/journal.pone.0170374] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 01/04/2017] [Indexed: 11/18/2022] Open
Abstract
Virological and serological surveys have documented that H1N1/2009, avian-origin canine H3N2 (cH3N2), seasonal human-origin H3N2 (hH3N2), and equine-origin H3N8 influenza viruses are consistently circulating in dogs. In the present study, a multiplex reverse-transcriptase polymerase chain reaction (mRT-PCR) assay was developed for simultaneous detection and differentiation of these influenza viruses. Four primer sets were designed to target the hemagglutinin genes of H1N1/2009, cH3N2, hH3N2, and H3N8 canine influenza viruses (CIVs). This mRT-PCR assay demonstrated high specificity and sensitivity for the four CIV subtypes. Additionally, mRT-PCR results obtained from 420 clinical samples were consistent with those obtained by the conventional virus isolation method. Our mRT-PCR assay is reliable for clinical diagnosis and rapid identification of CIVs.
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Affiliation(s)
- Chenxi Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qian Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Junyi Hu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Honglei Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Juan Pu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jinhua Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yipeng Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
- * E-mail:
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Wei YD, Gao WH, Sun HL, Yu CF, Pei XY, Sun YP, Liu JH, Pu J. A duplex RT-PCR assay for detection of H9 subtype avian influenza viruses and infectious bronchitis viruses. JOURNAL OF INTEGRATIVE AGRICULTURE : JIA 2016; 15:2105-2113. [PMID: 32288952 PMCID: PMC7128909 DOI: 10.1016/s2095-3119(15)61316-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/02/2016] [Indexed: 06/11/2023]
Abstract
H9 subtype avian influenza virus (AIV) and infectious bronchitis virus (IBV) are major pathogens circulating in poultry and have resulted in great economic losses due to respiratory disease and reduced egg production. As similar symptoms are elicited by the two pathogens, it is difficult for their differential diagnosis. So far, no reverse transcription-polymerase chain reaction (RT-PCR) assay has been found to differentiate between H9 AIV and IBV in one reaction. Therefore, developing a sensitive and specific method is of importance to simultaneously detect and differentiate H9 AIV and IBV. In this study, a duplex RT-PCR (dRT-PCR) was established. Two primer sets target the hemagglutinin (HA) gene of H9 AIV and the nucleocapsid (N) gene of IBV, respectively. Specific PCR products were obtained from all tested H9 AIVs and IBVs belonging to the major clades circulating in China, but not from AIVs of other subtypes or other infectious avian viruses. The sensitivity of the dRT-PCR assay corresponding to H9 AIV, IBV and mixture of H9 AIV and IBV were at a concentration of 1×101, 1.5×101 and 1.5×101 50% egg infective doses (EID50) mL-1, respectively. The concordance rates between the dRT-PCR and virus isolation were 99.1 and 98.2%, respectively, for detection of samples from H9N2 AIV or IBV infected chickens, while the concordance rate was 99.1% for detection of samples from H9N2 AIV and IBV co-infected chickens. Thus, the dRT-PCR assay reported herein is specific and sensitive, and suitable for the differential diagnosis of clinical infections and surveillance of H9 AIVs and IBVs.
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Affiliation(s)
- Yan-di Wei
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture/College of Veterinary Medicine/State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, P.R.China
| | - Wei-Hua Gao
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture/College of Veterinary Medicine/State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, P.R.China
| | - Hong-Lei Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture/College of Veterinary Medicine/State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, P.R.China
| | - Chen-Fang Yu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture/College of Veterinary Medicine/State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, P.R.China
| | - Xing-Yao Pei
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture/College of Veterinary Medicine/State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, P.R.China
| | - Yi-Peng Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture/College of Veterinary Medicine/State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, P.R.China
| | - Jin-Hua Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture/College of Veterinary Medicine/State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, P.R.China
| | - Juan Pu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture/College of Veterinary Medicine/State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, P.R.China
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Qin ZF, Sun J, Lu TK, Zeng SL, Hua QY, Ling QY, Chen SK, Lv JQ, Zhang CH, Cheng B, Ruan ZX, Bi YZ, Giambrone JJ, Wu HZ. Subtyping animal influenza virus with general multiplex RT-PCR and Liquichip high throughput (GMPLex). Virol Sin 2012; 27:120-31. [PMID: 22492003 DOI: 10.1007/s12250-012-3232-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 03/05/2012] [Indexed: 11/24/2022] Open
Abstract
This study developed a multiplex RT-PCR integrated with luminex technology to rapidly subtype simultaneously multiple influenza viruses. Primers and probes were designed to amplify NS and M genes of influenza A viruses HA gene of H1, H3, H5, H7, H9 subtypes, and NA gene of the N1 and N2 subtypes. Universal super primers were introduced to establish a multiplex RT-PCR (GM RT-PCR). It included three stages of RT-PCR amplification, and then the RT-PCR products were further tested by LiquiChip probe, combined to give an influenza virus (IV) rapid high throughput subtyping test, designated as GMPLex. The IV GMPLex rapid high throughput subtyping test presents the following features: high throughput, able to determine the subtypes of 9 target genes in H1, H3, H5, H7, H9, N1, and N2 subtypes of the influenza A virus at one time; rapid, completing the influenza subtyping within 6 hours; high specificity, ensured the specificity of the different subtypes by using two nested degenerate primers and one probe, no cross reaction occurring between the subtypes, no non-specific reactions with other pathogens and high sensitivity. When used separately to detect the product of single GM RT-PCR for single H5 or N1 gene, the GMPLex test showed a sensitivity of 10⁻⁵(= 280ELD₅₀) forboth tests and the Luminex qualitative ratio results were 3.08 and 3.12, respectively. When used to detect the product of GM RT-PCR for H5N1 strain at the same time, both showed a sensitivity of 10⁻⁴(=2800 ELD₅₀). The GMPLex rapid high throughput subtyping test can satisfy the needs of influenza rapid testing.
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Affiliation(s)
- Zhi-feng Qin
- Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen 518010, China.
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Tang Q, Wang J, Bao J, Sun H, Sun Y, Liu J, Pu J. A multiplex RT-PCR assay for detection and differentiation of avian H3, H5, and H9 subtype influenza viruses and Newcastle disease viruses. J Virol Methods 2012; 181:164-9. [PMID: 22387341 DOI: 10.1016/j.jviromet.2012.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 01/31/2012] [Accepted: 02/13/2012] [Indexed: 11/24/2022]
Abstract
Avian influenza viruses (AIVs) and Newcastle disease viruses (NDVs) co-circulate in the poultry population in China. These viruses cause repeated disease outbreaks that exhibit similar clinical symptoms and epidemiological patterns. H5 and H9 influenza viruses are the major pathogens infecting poultry stocks. Recently, H3 AIV (one of the main subtypes in waterfowl) has become endemic in chickens. A multiplex reverse-transcriptase polymerase chain reaction (mRT-PCR) assay was designed for simultaneous detection and differentiation of avian H3, H5, H9 subtype AIVs and NDVs. Four primer sets were evaluated, three of which specifically targeted the hemagglutinin genes of H3, H5 and H9 AIVs, while the other targeted the NDV fusion gene. The sensitivity and specificity of the mRT-PCR assay was determined. The assay detected the major clades or genotypes of all of the reference AIVs and NDVs currently circulating in China. In addition, the mRT-PCR results obtained from screening 380 clinical swabs and 12 experimental tracheal samples were consistent with those obtained using conventional virus isolation methods. The mRT-PCR assay was established successfully for the detection and differentiation of avian H3, H5, and H9 subtype AIVs and NDVs. The method should, therefore, provide a valuable diagnostic tool for these infections.
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Affiliation(s)
- Qingdong Tang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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Rapid detection of avian influenza virus in chicken fecal samples by immunomagnetic capture reverse transcriptase-polymerase chain reaction assay. Diagn Microbiol Infect Dis 2011; 69:258-65. [PMID: 21353948 DOI: 10.1016/j.diagmicrobio.2010.09.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 09/09/2010] [Accepted: 09/29/2010] [Indexed: 11/22/2022]
Abstract
Avian influenza virus (AIV) causes great economic losses for the poultry industry worldwide and threatens the human population with a pandemic. The conventional detection method for AIV involves sample preparation of viral RNA extraction and purification from raw sample such as bird droppings. In this study, magnetic beads were applied for immunoseparation and purification of AIV from spiked chicken fecal sample. The beads were conjugated with monoclonal antibodies against the AIV nucleoprotein, which is conserved in all the AIV. The bead-captured virus was detected by reverse transcriptase-polymerase chain reaction (RT-PCR) without RNA extraction because of effective removal of RT-PCR inhibitors. The developed bead-based assay showed a similar detection limit comparable to the RNA extraction and the classic virus isolation method. Using ready-to-use antibody-conjugated bead, the method requires less than 5 h. Furthermore, the method has potential to integrate into a Lab-on-a-chip system for rapid detection and identification of AIV.
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