Genome Sequences of Newly Emerged Newcastle Disease Virus Strains Isolated from Disease Outbreaks in Indonesia.

Mohammad Rabiei,Farhid Hemmatzadeh,Jagoda Ignjatovic,Putri Pandarangga,Mohammed Alsharifi,Mohamad Indro Cahyono,Risa Indriani,Indi Dharmayanti,Phuong Thi Kim Doan,Rick Tearle,Simson Tarigan,Wai Yee Low,Milton M Mcallister,Simon Roux

doi:10.1128/mra.00204-20

Abstract

Here, we report two genomes of newly emerged strains of Newcastle disease virus (NDV), Chicken/Indonesia/Tangerang/004WJ/14 and Chicken/Indonesia/VD/003WJ/11, from disease outbreaks in chickens in Indonesia. Phylogenetic study results of the fusion (F) protein's gene-coding sequences of different genotypes of NDV revealed that these two strains belong to genotype VII.1 in the class II cluster of avian paramyxoviruses.

Highlights

We report two genomes of newly emerged strains of Newcastle disease virus (NDV), Chicken/Indonesia/Tangerang/004WJ/14 and Chicken/Indonesia/ VD/003WJ/11, from disease outbreaks in chickens in Indonesia
Microbiology Resource Announcement nucleotide collection using NCBI BLAST, and two NDV contigs for Tangerang and VD were identified, with 46.52% and 46.49% genome GC contents, 15,096 and 15,179 nucleotide lengths, and 818-fold and 534-fold coverages, respectively. These contigs were compared to the Indonesian genotype VII strain Chicken/Sukorejo/019/10 (Sukorejo; GenBank accession number HQ697255.1) and showed similarities of 97.90% and 98.95%, respectively
In the contig of Tangerang, some contaminating sequences of Pseudomonas spp. were observed after an NCBI BLAST search at the end of the sequence; they were removed with BioEdit, and reverse transcriptase PCR (RT-PCR; OneStep Ahead RT-PCR, Qiagen, USA) and Sanger sequencing were used to close the detected gaps in this sequence after alignment to Sukorejo (GenBank accession number HQ697255.1)

Summary

GENOME SEQUENCES crossm

Mohammad Rabiei,a Mohamad Indro Cahyono,a,b Phuong Thi Kim Doan,a,c Putri Pandarangga,a,d Simson Tarigan,b Risa Indriani,b Indi Dharmayanti,b Jagoda Ignjatovic,e Wai Yee Low,f Rick Tearle,f Milton M. Mohammed Alsharifi,g Farhid Hemmatzadeha aSchool of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia bIndonesian Research Centre for Veterinary Science, Bogor, West Java, Indonesia cSchool of Animal and Veterinary Sciences, Tay Nguyen University, Dak Lak, Vietnam dDepartment of Veterinary Pathology, Nusa Cendana University, Kupang, Indonesia eSchool of Veterinary Science, The University of Melbourne, Melbourne, Victoria, Australia fDavies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia gResearch Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia

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