First Isolation and Rapid Identification of Newcastle Disease Virus from Aborted Fetus of Dromedary Camel Using Next-Generation Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Viral Culture
2.2. Hemagglutination (HA) Test
2.3. Preparation of Sample for Illumina Sequencing
2.4. Library Construction for Illumina Sequencing
2.5. Analysis of Sequence Reads and Genome Assembly
2.6. Comparative Genome Analysis and Phylogenetic Analysis
2.7. Genome Sequencing of Newcastle Disease Virus (NDV) Isolated from Dromedary Camel (DcNDV)
3. Results
3.1. Necropsy
3.2. Virus Culture and Haemagglutination (HA) Test
3.3. Deep Sequence Analysis
3.4. Genome Analysis
3.5. Phylogenetic Analysis
3.6. Nucleotide Sequence GenBank Accession Number
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
- Rahman, A.; Habib, M.; Shabbir, M.Z. Adaptation of Newcastle Disease Virus (NDV) in Feral Birds and their Potential Role in Interspecies Transmission. Open Virol. J. 2018, 12, 52–68. [Google Scholar] [CrossRef] [PubMed]
- Elmberg, J.; Berg, C.; Lerner, H.; Waldenstrom, J.; Hessel, R. Potential disease transmission from wild geese and swans to livestock, poultry and humans: A review of the scientific literature from a One Health perspective. Infect. Ecol. Epidemiol. 2017, 7, 1300450. [Google Scholar] [CrossRef] [PubMed]
- Alexander, D.J. Newcastle disease in the European Union 2000 to 2009. Avian Pathol. 2011, 40, 547–558. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Alexander, D.J.; Parsons, G.; Marshall, R. Infection of fowls with Newcastle disease virus by food contaminated with pigeon faeces. Vet. Rec. 1984, 115, 601–602. [Google Scholar] [CrossRef] [PubMed]
- Zhao, P.; Sun, L.; Sun, X.; Li, S.; Zhang, W.; Pulscher, L.A.; Xing, M. Newcastle disease virus from domestic mink, China, 2014. Vet. Microbiol. 2017, 198, 104–107. [Google Scholar] [CrossRef] [PubMed]
- Sharma, B.; Pokhriyal, M.; Rai, G.K.; Saxena, M.; Ratta, B.; Chaurasia, M.; Mondal, B. Isolation of Newcastle disease virus from a non-avian host (sheep) and its implications. Arch. Virol. 2012, 157, 1565–1567. [Google Scholar] [CrossRef] [PubMed]
- Yates, V.J.; Fry, D.E.; Henderson, B.W., Jr. Isolation of Newcastle Disease virus from a calf. J. Am. Vet. Med. Assoc. 1952, 120, 149–150. [Google Scholar] [PubMed]
- He, Y.; Taylor, T.L.; Dimitrov, K.M.; Butt, S.L.; Stanton, J.B.; Goraichuk, I.V.; Afonso, C.L. Whole-genome sequencing of genotype VI Newcastle disease viruses from formalin-fixed paraffin-embedded tissues from wild pigeons reveals continuous evolution and previously unrecognized genetic diversity in the U.S. Virol. J. 2018, 15. [Google Scholar] [CrossRef]
- Bello, M.B.; Yusoff, K.M.; Ideris, A.; Hair-Bejo, M.; Peeters, B.P.H.; Jibril, A.H.; Omar, A.R. Genotype Diversity of Newcastle Disease Virus in Nigeria: Disease Control Challenges and Future Outlook. Adv. Virol. 2018, 2018, 1–17. [Google Scholar] [CrossRef] [Green Version]
- Mayahi, V.; Esmaelizad, M. Molecular evolution and epidemiological links study of Newcastle disease virus isolates from 1995 to 2016 in Iran. Arch. Virol. 2017, 162, 3727–3743. [Google Scholar] [CrossRef]
- Dimitrov, K.M.; Ramey, A.M.; Qiu, X.; Bahl, J.; Afonso, C.L. Temporal, geographic, and host distribution of avian paramyxovirus 1 (Newcastle disease virus). Infect. Genet. Evol. 2016, 39, 22–34. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Sun, C.; Wen, H.; Chen, Y.; Chu, F.; Lin, B.; Ren, G.; Song, Y.; Wang, Z.; Lin, B. Roles of the highly conserved amino acids in the globular head and stalk region of the Newcastle disease virus HN protein in the membrane fusion process. Biosci. Trends 2015, 9, 56–64. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Abu Elzein, E.; Hassanein, M.; Al Afaleq, A. High level agglutination of camel (Camelus dromedarius) erythrocytes by avian paramyxovirus serotype 1. Avian Pathol. 1993, 22, 189–192. [Google Scholar] [CrossRef] [PubMed]
- Wernery, U.; Corman, V.; Wong, E.; Tsang, A.; Muth, D.; Lau, S.; Khazanehdari, K.; Zirkel, F.; Ali, M.; Nagy, P.; et al. Acute Middle East Respiratory Syndrome Coronavirus Infection in Livestock Dromedaries, Dubai, 2014. Emerg. Infect. Dis. 2015, 21, 1019–1022. [Google Scholar] [CrossRef] [PubMed]
- OIE—World Organisation for Animal Health. (2019). Retrieved 16 August 2019. Available online: https://web.oie.int/boutique/index.php?page=ficprod&id_produit=1554&lang=en (accessed on 16 August 2019).
- Guan, T.P.; Teng, J.L.L.; Yeong, K.Y.; You, Z.Q.; Liu, H.; Wong, S.S.Y.; Woo, P.C.Y. Metagenomic analysis of Sichuan takin fecal sample viromes reveals novel enterovirus and astrovirus. Virology 2018, 521, 77–91. [Google Scholar] [CrossRef] [PubMed]
- Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30, 2114–2120. [Google Scholar] [CrossRef] [PubMed]
- Schmieder, R.; Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011, 27, 863–864. [Google Scholar] [CrossRef] [Green Version]
- Fu, L.; Niu, B.; Zhu, Z.; Wu, S.; Li, W. CD-HIT: Accelerated for clustering the next-generation sequencing data. Bioinformatics 2012, 28, 3150–3152. [Google Scholar] [CrossRef]
- Manual, B. BLAST® Command Line Applications User Manual. Available online: https://www.ncbi.nlm.nih.gov/books/NBK279690/ (accessed on 1 February 2019).
- Huson, D.H.; Beier, S.; Flade, I.; Górska, A.; El-Hadidi, M.; Mitra, S.; Tappu, R. MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Comput. Biol. 2016, 12. [Google Scholar] [CrossRef]
- Chevreux, B.; Wetter, T.; Suhai, S. Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics 1999, Hannover, Germany. Comput. Sci. Biol. 1999, 45–56. [Google Scholar] [CrossRef]
- ORF Finder (Open Reading Frame). Available online: https://www.ncbi.nlm.nih.gov/orffinder/ (accessed on 2 February 2019).
- Edgar, R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32, 1792–1797. [Google Scholar] [CrossRef] [PubMed]
- Kumar, S.; Stecher, G.; Li, M.; Knyaz, C.; Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 2018, 35, 1547–1549. [Google Scholar] [CrossRef] [PubMed]
- Joseph, S.; Xie, J.; Wernery, U.; Jose, S.; Fan, R.Y.Y.; Woo, P.C.Y.; Yuen, K.-Y. A novel astrovirus from dromedaries in the Middle East. J. Gen. Virol. 2015, 96, 2697–2707. [Google Scholar] [CrossRef] [Green Version]
- Hall, T. BioEdit: An important software for molecular biology. Gerf Bull. Biosci. 2011, 2, 60–61. [Google Scholar]
- Qiu, X.; Meng, C.; Zhan, Y.; Yu, S.; Li, S.; Ren, T.; Ding, C. Phylogenetic, antigenic and biological characterization of pigeon paramyxovirus type 1 circulating in China. Virol. J. 2017, 14. [Google Scholar] [CrossRef]
- Akhtar, S.; Muneer, M.A.; Muhammad, K.; Tipu, M.Y.; Rabbani, M.; ul-Rahman, A.; Shabbir, M.Z. Genetic characterization and phylogeny of pigeon paramyxovirus isolate (PPMV-1) from Pakistan. SpringerPlus 2016, 5. [Google Scholar] [CrossRef]
- Jin, J.; Zhao, J.; Ren, Y.; Zhong, Q.; Zhang, G. Contribution of HN protein length diversity to Newcastle disease virus virulence, replication and biological activities. Sci. Rep. 2016, 6. [Google Scholar] [CrossRef]
- Rohaim, M.; El Naggar, R.; Helal, A.; Hussein, H.; LeBlanc, N. Genetic Characterization of Pigeon Paramyxovirus Type 1 in Egypt. Br. J. Virol. 2016, 3, 27–32. [Google Scholar] [CrossRef]
- Sabra, M.; Dimitrov, K.M.; Goraichuk, I.V.; Wajid, A.; Sharma, P.; Williams-Coplin, D.; Afonso, C.L. Phylogenetic assessment reveals continuous evolution and circulation of pigeon-derived virulent avian avulaviruses 1 in Eastern Europe, Asia, and Africa. BMC Vet. Res. 2017, 13. [Google Scholar] [CrossRef]
- Aldous, E.; Fuller, C.; Ridgeon, J.; Irvine, R.; Alexander, D.; Brown, I. The Evolution of Pigeon Paramyxovirus Type 1 (PPMV-1) in Great Britain: A Molecular Epidemiological Study. Transbound. Emerg. Dis. 2012, 61, 134–139. [Google Scholar] [CrossRef]
- Welch, C.N.; Shittu, I.; Abolnik, C.; Solomon, P.; Dimitrov, K.M.; Taylor, T.L.; Williams-Coplin, D.; Goraichuk, I.V.; Meseko, C.A.; Ibu, J.O.; et al. Genomic comparison of Newcastle disease viruses isolated in Nigeria between 2002 and 2015 reveals circulation of highly diverse genotypes and spillover into wild birds. Arch. Virol. 2019, 164, 2031–2047. [Google Scholar] [CrossRef] [PubMed]
- Wernery, U.; Lau, S.K.P.; Woo, P.C.Y. Middle East respiratory syndrome (MERS) coronavirus and dromedaries. Vet. J. 2017. [Google Scholar] [CrossRef] [PubMed]
- Han, H.J.; Yu, H.; Yu, X.J. Evidence for zoonotic origins of Middle East respiratory syndrome coronavirus. J. Gen. Virol. 2016. [Google Scholar] [CrossRef] [PubMed]
- Woo, P.C.Y.; Lau, S.K.P.; Fan, R.Y.Y.; Lau, C.C.Y.; Wong, E.Y.M.; Joseph, S.; Yuen, K.Y. Isolation and characterization of dromedary camel coronavirus UAE-HKU23 from dromedaries of the middle east: Minimal serological cross-reactivity between MERS coronavirus and dromedary camel coronavirus UAE-HKU23. Int. J. Mol. Sci. 2016, 17, 691. [Google Scholar] [CrossRef] [PubMed]
- Sridhar, S.; Teng, J.L.L.; Chiu, T.H.; Lau, S.K.P.; Woo, P.C.Y. Hepatitis E virus genotypes and evolution: Emergence of camel hepatitis E variants. Int. J. Mol. Sci. 2017, 18, 869. [Google Scholar] [CrossRef] [PubMed]
- Lee, G.H.; Tan, B.H.; Teo, C.-Y.; Lim, S.G.; Dan, Y.Y.; Wee, A.; Teo, C.G. Chronic Infection with Camelid Hepatitis e Virus in a Liver Transplant Recipient Who Regularly Consumes Camel Meat and Milk. Gastroenterology 2016, 150, 355–357.e3. [Google Scholar] [CrossRef] [PubMed]
- Rasche, A.; Saqib, M.; Liljander, A.M.; Bornstein, S.; Zohaib, A.; Renneker, S.; Corman, V.M. Hepatitis E virus infection in dromedaries, North and East Africa, United Arab Emirates, and Pakistan, 1983–2015. Emerg. Infect. Dis. 2016, 22, 1249–1252. [Google Scholar] [CrossRef] [PubMed]
- Woo, P.C.Y.; Lau, S.K.P.; Teng, J.L.L.; Tsang, A.K.L.; Joseph, M.; Wong, E.Y.M.; Yuen, K.Y. New hepatitis E virus genotype in camels, the Middle East. Emerg. Infect. Dis. 2014, 20, 1044–1048. [Google Scholar] [CrossRef]
- Woo, P.C.Y.; Lau, S.K.P.; Li, T.; Jose, S.; Yip, C.C.Y.; Huang, Y.; Yuen, K.Y. A novel dromedary camel enterovirus in the family Picornaviridae from dromedaries in the Middle East. J. Gen. Virol. 2015, 96, 1723–1731. [Google Scholar] [CrossRef]
- Woo, P.C.Y.; Lau, S.K.P.; Tsoi, H.W.; Patteril, N.G.; Yeung, H.C.; Joseph, S.; Yuen, K.Y. Two novel dromedary camel bocaparvoviruses from dromedaries in the middle east with unique genomic features. J. Gen. Virol. 2017, 98, 1349–1359. [Google Scholar] [CrossRef]
- Woo, P.C.Y.; Lau, S.K.P.; Teng, J.L.L.; Tsang, A.K.L.; Joseph, M.; Wong, E.Y.M.; Yuen, K.Y. Metagenomic analysis of viromes of dromedary camel fecal samples reveals large number and high diversity of circoviruses and picobirnaviruses. Virology 2014, 471–473, 117–125. [Google Scholar] [CrossRef] [PubMed]
- Woo, P.C.Y.; Lau, S.K.P.; Teng, J.L.L.; Cao, K.-Y.; Wernery, U.; Schountz, T.; Yuen, K.-Y. New Hepatitis E Virus Genotype in Bactrian Camels, Xinjiang, China, 2013. Emerg. Infect. Dis. 2016, 22, 2219–2221. [Google Scholar] [CrossRef] [PubMed]
- Joseph, S.; Wernery, U.; Teng, J.L.; Wernery, R.; Huang, Y.; Patteril, N.A.; Woo, P.C. First isolation of West Nile virus from a dromedary camel. Emerg. Microbes Infect. 2016, 5. [Google Scholar] [CrossRef] [PubMed]
Strains/Genotypes | Cleavage Site Motif | Fusion Peptide | Heptad Repeats | Cysteine Residues | Transmembrane Domain | ||
---|---|---|---|---|---|---|---|
HRa | HRb | HRc | |||||
112–117 | 117–142 | 143–185 | 268–299 | 471–500 | 501–521 | ||
DcNDV | KRQKRF | FIGAIIGSVALGVATSAQITAAAAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLAVAVGKMQQF | LYDSQTQLLGIQVNLPSVGNLNNMR | NNSISNALDRLAESNSKLDKVNVKLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIILTVISLIFGALSLIL |
Avian/Australia/I-2/2005/I | RKQGRL | LIGAIIGGVALGVATAAQITAASAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLAVAVGKMQQF | LYDSQTQLLGIQVILPSVGNLNNMR | NNSISNALDKLEESNSKLDKVNVKLASTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTVISLICGILSLVL |
Mink/China/Y19/2014/II | GRQGRL | LIGAIIGGVALGVATAAQITAAAAL | QAKQNAANILRLKESIAATNEAVHEVTDGLSQLAVAVGKMQQF | LYDSQTQLLGIQVTLPSVGNLNNMR | NNSTSNALNKLEESNSKLDKVNVKLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTIISLVFGILSLVL |
Avian/China/Mukteswar/2007/III | RRQRRF | FIGAIIGGVALGVATAAQITAASAL | QANQNAANILRLKESIAATNEAVHEVTGGLSQLAVAVGKMQQF | FYDSQTQLLGIQVTLPSVGNLNNMR | NHSISNALDKLEESNSKLDKVNVRLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTVISLVLGMLSLVL |
Chicken/UnitedKingdom/Herts/1933/IV | RRQRRF | FIGAIIGGVALGVATAAQITAASAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLAVAVGKMQQF | LYDSQTQILGIQVTLPSVGNLNNMR | NNSISNALNKLEESNSKLDKVNVRLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTVISLVFGVLSLVL |
Gamefowl/USA/CA/211472/2002/V | RRQKRF | FVGAIIGGVALGVATAAQITAAAAL | QANQNAANILRLKESIAATNDAVHEVTNGLSQLAVAVGKMQQF | LYDSQTQLLGIQINLPSVGSLNNMR | NNSISSTLDKLAESNNKLNKVNVNLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLAIVSLAFGVISLVL |
Pigeon/Egypt/ElFayom/79/1112/2015/VI | KRQKRF | FIGAIIGSVALGVATSAQITAAAAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLAVAVGKMQQF | LYDSQTQLLGIQVNLPSVGNLNNMR | NNSISNALDRLAESNSKLDKVNVKLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTVISLVFGALSLIL |
Mink/China/mNDV-01-HLJ/2014/VII | RRQKRF | FIGAIIGSVALGVATAAQITAAAAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLSVAVGKMQQF | LYDSQTQLLGIQVNLPSVGNLNNMR | NNSISNALDKLAESNSKLEKVNVRLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTVISLVFGALSLGL |
Chicken/China/QH1/1979/VIII | RRQKRF | FIGAVIGSVALGVATAAQITAAAAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLSVAVGKMQQF | LYDSQTQLLGIQVTLPSVGNLNNMR | NNSISNALDKLSESNSKLDKVNVKLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LIIYIVLIVISLVSGVLSLVL |
Chicken/China/F48E8/1946/IX | RRQRRF | FIGAVIGSVALGVATAAQITAASAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLSVAVGKMQQF | LYDSQTQLLGIQVTLPSVGNLNNMR | NNSISNALDKLEESNSKLDKVNVKLTGTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTIISLVCGILSLVL |
Mallard/USA/Ohio/04-411/2004/X | EKQGRL | LIGAIIGGVALGVATAAQITAASAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLSVAVGKMQQF | LYDSQTQLLGIQVTLPSVGNLNNMR | NNSISNALDKLEESNSKLDKVNVKLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIILTVVSLVCGILSLVL |
Chicken/Madagascar/MG/725/2008/XI | RRRRRF | FVGAIIGSVALGVATAAQITAAAAL | QAKQNAANILRLKESIAATNEAVHEVTDGLSQLSVAVGKMQQF | LYDSQTQILGIQVTMPSVGSLNNMR | NNSISKTLNKLEESNSKLDRVNVKLASTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTVVSLVFGVLSLVL |
Peacock/Peru/2011/XII | RRQKRF | FIGAVIGSVALGVATAAQITAAAAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLSVAVGKMQQF | LYDSQTQLLGIQVNLPSVGNLNNMR | NNSISNALDKLAESNSKLDKINVRLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTAISLVFGTLSLVL |
Chicken/Zambia/Chiwoko/2015/XIII | RRQKRF | FIGAVIGSVALGVATAAQITAAAAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLSVAVGKMQQF | LYDSQTQLLGIQVNLPSVGNLNNMR | NNSISNALDKLAESNNKLDKVNVRLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTVTSLVFGALSLAL |
Duck/Nigeria/NG-695/KG.LOM.11-16/2009/XIV | RRRKRF | FVGAVIGSVALGVATAAQVTAAAAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLSVAVGKMQQF | LYDPQTQLLGIQVNLPSVGNLNNMR | NNSISNALDKLAESNNKLDKVNVRLTSASA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTGLSLMFGTLSLVL |
Chicken/DominicanReplubic/JuanLopez/499-31/2008/XVI | RRQKRF | FVGAIIGGVALGVATAAQITAAAAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLSVAVGKMQQF | LYDPQTQLLGIQVTLPSVGNLNNMR | NNSISNALSKLAESNSKLSKVNVKLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTVVSLAFGVISLVL |
Chicken/Nigeria/NIE08-1365/2008/XVII | RRQKRF | FIGAVIGSVALGVATAAQITAAAAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLSVAVGKMQQF | LYDSQTQLLGIQVSLPSVGNLNNMR | NNSISSALDKLAESNSKLDKVNVRLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTVVSLVFGTLSLVL |
Chicken/IvoryCoast/CIV08-026/2007/XVIII | RRQKRF | FVGAVIGSVALGVATAAQITAAAAL | QANQNAANILRLKESIAATNEAVHEVTDGLSQLSVAVGKMQQF | LYDSQTQLLGIQVSLPSVGNLNNMR | NNSISNALDKLAESNSKLDKVNVRLTSTSA | 25, 27, 76, 199, 338, 347, 362, 370, 394, 399, 401, 424, 523 | LITYIVLTVISLVFGTLSLIL |
Strains/Genotypes | Transmembrane Domain | Heptad Repeats | Receptor Recognition | N-linked Glycosylation Sites | Cysteine Residues | |
---|---|---|---|---|---|---|
HRa | HRb | |||||
25–45 | 74–88 | 96–110 | 174, 175, 198, 236, 258, 299, 317, 401, 416, 498, 526, 547 | |||
DcNDV | FRIAVLFLVVMTLAISAAVL | LGSNQDVVDRIYKQV | LLNTESVIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 508, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Avian/Australia/I-2/2005/I | FRIAILFLTVVTLAVSAAAL | LGSNQDVVDRIYKQV | LLNTESTIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Mink/China/Y19/2014/II | FRIAILLLTIVTLAISVISL | LGSNQDVVDRIYKQV | LLSTETTIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 538 | 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Avian/China/Mukteswar/2007/III | FRIAALLLMVITLAVSAVAL | LGSNQDVVDRIYKQV | LLNTESIIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 508, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Chicken/UnitedKingdom/Herts/1933/IV | FRIAILLLIVITLAISAAAL | LSSNQDVVDRIYKQV | LLNTESVIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 508, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Gamefowl/USA/CA/211472/2002/V | FRVAVLSLIVMTLAISVAAL | LNSNQDVVDRVYKQV | LLNTESIIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Pigeon/Egypt/ElFayom/79/1112/2015/VI | FRITVLLLVVMTLAISAAVL | LGSNQDVVDRIYKQ | LLNTESIIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 508, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Mink/China/mNDV-01-HLJ/2014/VII | FRIAVLLLMVMTLAISAAAL | LSSSQDVIDRIYKQV | LLNTKSIIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 508, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Chicken/China/QH1/1979/VIII | FRIAVLFLIVTTLAISAAAL | LSSNQDVVDRIYKQV | LLNTESIIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 508, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Chicken/China/F48E8/1946/IX | FRTAVILLIVVTFSISAAAL | LGSNQDVVDRIYKQV | LLNTESIIMSAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 508, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Mallard/USA/Ohio/04-411/2004/X | FRIAILLLTVVTLAISAAAL | LGSNQDVVDRIYKQV | LLNTESTIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Chicken/Madagascar/MG/725/2008/XI | FRIAILLLITITLALSTAAL | LSSNRDVMDRVYKQV | LLSTESVIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 508, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Peacock/Peru/2011/XII | FRVSVLLLMVMTLAISAVAL | LSSSQDVIDRIYKQV | LLNTESIIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Chicken/Zambia/Chiwoko/2015/XIII | FRTAVLLLIVMTLAISIAAL | LSSSQDVVDRIYKQV | LLNTESVIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Duck/Nigeria/NG-695/KG.LOM.11-16/2009/XIV | FRIAVLLLMVMTLAISAAAL | LGSSQDVIDRIYKQV | LLNTESIIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 508, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Chicken/DominicanReplubic/JuanLopez/499-31/2008/XVI | FRITVLLFILMTLAISVATL | LGSNQDVVDRIYKQV | LLNTESIIMNALTSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 508, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Chicken/Nigeria/NIE08-1365/2008/XVII | FRVAVLLLIAVTLAVSAAAL | LSSSQDVIDRIYKQV | LLNTESILMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 508, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Chicken/IvoryCoast/CIV08-026/2007/XVIII | FRIAVLFLMTMTFVISAAAL | LSSSQDVIDRIYKQV | LLNTESIIMNAITSL | R, I, D, K, E, Y, Y, E, R, R, Y, E | 119, 341, 433, 481, 508, 538 | 123, 172, 186, 196, 238, 247, 251, 344, 455, 461, 465, 531, 542 |
Strains/Genotypes | Neutralizing Epitopes | C-terminal Domains | |||
---|---|---|---|---|---|
193–211 | 345–355 | 494 | 513–521 | 569 | |
DcNDV | LSGCRDHSHSHQYLALGV | PDEQSYQIRMA | D | RVTRVSSGS | D |
Avian/Australia/I-2/2005/I | LSGCRDHSHSHQYLALGV | PDEQDYQIRMA | D | RITRVSSGS | D |
Mink/China/Y19/2014/II | LSGCRDHSHSHQYLALGV | PDEQDYQIRMA | G | RITRVSSSS | D |
Avian/China/Mukteswar/2007/III | LSGCRDHTHSHQYLALGV | PDEQDYQIRMA | D | RITRVSSSS | G |
Chicken/UnitedKingdom/Herts/1933/IV | LSGCRDHSHSHQYLALGV | PDEQDYQIRMA | D | RITRVSSRS | D |
Gamefowl/USA/CA/211472/2002/V | LSGCRDHSHSHQYLALGV | PDEQDYQVRMA | N | RITRVSSTS | D |
Pigeon/Egypt/ElFayom/79/1112/2015/VI | LSGCRDHSHSHQYLALGV | PDEQSYQIRMA | D | RVTRVSSGS | D |
Mink/China/mNDV-01-HLJ/2014/VII | LSGCRDHSHSHQYLALGV | PDEQDYQIRMA | D | RVTRVSSSS | D |
Chicken/China/QH1/1979/VIII | LSGCRDHSHSHQYLALGV | PDEQDYQIRMA | D | RMTRVSSSS | D |
Chicken/China/F48E8/1946/IX | LSGCRDHSHSHQYLALGV | PDEQDYQIRMA | D | RITRVSSSS | D |
Mallard/USA/Ohio/04-411/2004/X | LSGCRDHSHSYQYLALGV | PDEQDYQIRMA | D | RITRVSSSS | D |
Chicken/Madagascar/MG/725/2008/XI | LSGCRDHSHSHQYLALGV | PDEQDYQIRMA | D | RITRVSSSS | G |
Peacock/Peru/2011/XII | LSGCRDHSHSHQYLALGV | PDEQDYQIRMA | G | RVTRVSSSS | D |
Chicken/Zambia/Chiwoko/2015/XIII | LSGCRDHSHSHQYLALGV | PDEQDYQIRMA | D | RVTRVSSSS | A |
Duck/Nigeria/NG-695/KG.LOM.11-16/2009/XIV | LSGCRDHSHSHQYLALGV | PDEQDYQIRMA | D | RVTRVSSSS | D |
Chicken/DominicanReplubic/JuanLopez/499-31/2008/XVI | LSGCRDHSHSHQYLALGV | PDEQDYQIRMA | D | RITRVSSSS | D |
Chicken/Nigeria/NIE08-1365/2008/XVII | LSGCRDHSHSHQYLALGV | PDEQDHQIRMA | D | HVTRVSSSS | D |
Chicken/IvoryCoast/CIV08-026/2007/XVIII | LSGCRDHSHSHQYLALGV | PDEQDYQIRMA | D | RVTRVSSSS | D |
Reference Strains | Accession | Genotype Nucleotide Differences (%) with DcNDV | |||||||
---|---|---|---|---|---|---|---|---|---|
Number | N | P | M | F | HN | L | Concatenated Genes | ||
Pigeon/China/SH/0167/2013 | KT163262 | VIa | 90.7 | 86.5 | 90.3 | 90.4 | 88.1 | 91.4 | 90.3 |
Pigeon/USA/Maryland/1984 | FJ410147 | VIb | 92.9 | 89.2 | 92.5 | 92.2 | 91.1 | 93.3 | 92.4 |
Crested ibis/China/Shaanxi10/2010 | KC853020 | VIc | 90.5 | 87.7 | 90.0 | 91.0 | 89.0 | 90.9 | 90.3 |
Pigeon/China/SD/2012 | KJ808820 | VIe | 90.6 | 89.3 | 91.2 | 91.0 | 90.2 | 92.2 | 91.3 |
Pigeon/USA/PA/0712/2007 | KC013040 | VIf | 90.7 | 87.7 | 90.2 | 91.6 | 89.3 | 91.4 | 90.7 |
Pigeon/Egypt/El_Fayom/79/1112/2015 | KY042133 | VIg | 96.4 | 95.9 | 97.5 | 97.0 | 96.7 | 97.1 | 96.9 |
Pigeon/Egypt/Qena/56/1107/2015 | KY042131 | VIg | 96.5 | 95.3 | 97.0 | 97.1 | 96.4 | 97.2 | 96.8 |
Pigeon/Egypt/Giza/11/1088/2015 | KY042129 | VIg | 97.0 | 94.7 | 96.9 | 97.1 | 96.3 | 97.2 | 96.8 |
Pigeon/Russia/Vladimir/687/2005 | JF827026 | VIg | 97.3 | 96.5 | 97.4 | 96.9 | 96.8 | 98.8 | 97.8 |
Pigeon/Ukraine/Doneck/3/968/2007 | KY042128 | VIg | 97.0 | 95.9 | 96.9 | 96.8 | 96.2 | 97.6 | 97.1 |
Pigeon/Ukraine/Kharkiv/23-01/967/2013 | KY042127 | VIg | 96.7 | 95.4 | 96.5 | 96.5 | 96.0 | 97.3 | 96.8 |
Pigeon/Kenya/2012 | JX518532 | VIh | 86.7 | 86.3 | 90.1 | 90.6 | 88.8 | 91.4 | 89.9 |
Pigeon/China/SX-01/Ch/2015 | KX247376 | VIj | 91.2 | 87.7 | 91.0 | 90.3 | 88.1 | 91.0 | 90.3 |
Pigeon/Belgium/11-07574/2011 | JX901122 | VIk | 90.6 | 86.7 | 90.6 | 90.4 | 88.1 | 91.4 | 90.3 |
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Teng, J.L.L.; Wernery, U.; Lee, H.H.; Joseph, S.; Fung, J.; Elizabeth, S.K.; Yeong, K.Y.; Kinne, J.; Chan, K.-H.; Lau, S.K.P.; et al. First Isolation and Rapid Identification of Newcastle Disease Virus from Aborted Fetus of Dromedary Camel Using Next-Generation Sequencing. Viruses 2019, 11, 810. https://doi.org/10.3390/v11090810
Teng JLL, Wernery U, Lee HH, Joseph S, Fung J, Elizabeth SK, Yeong KY, Kinne J, Chan K-H, Lau SKP, et al. First Isolation and Rapid Identification of Newcastle Disease Virus from Aborted Fetus of Dromedary Camel Using Next-Generation Sequencing. Viruses. 2019; 11(9):810. https://doi.org/10.3390/v11090810
Chicago/Turabian StyleTeng, Jade Lee Lee, Ulrich Wernery, Hwei Huih Lee, Sunitha Joseph, Joshua Fung, Shyna Korah Elizabeth, Kai Yan Yeong, Joerg Kinne, Kwok-Hung Chan, Susanna Kar Pui Lau, and et al. 2019. "First Isolation and Rapid Identification of Newcastle Disease Virus from Aborted Fetus of Dromedary Camel Using Next-Generation Sequencing" Viruses 11, no. 9: 810. https://doi.org/10.3390/v11090810