Molecular phylogenetics of Newcastle disease viruses isolated from vaccinated flocks during outbreaks in Southern India reveals circulation of a novel sub‐genotype

Gowthaman, Vasudevan; Ganesan, Venkateswaran; Murthy, T R Gopala Krishna; Nair, Sowmya; Yegavinti, Nagarjuna; Saraswathy, Puzhavakath Vaidyanathan; Kumar, Ganesan Suresh; Udhayavel, Shanmugasunderam; Senthilvel, K.; Subbiah, Madhuri

doi:10.1111/tbed.13030

Cited by 19 publications

(23 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Two previously assigned sub-genotypes (Miller et al, 2015), were further split into two sub-genotypes each – XIIIa into XIII.1.1 and XIII.1.2, and XIIIb into XIII.2.1 and XIII.2.2, respectively (Supplemental Fig. S5B) because of the addition of new sequences from recent studies (Gowthaman et al, 2019; Mayahi and Esmaelizad, 2017). Viruses isolated from different countries in Africa between 1995 and 2015 formed sub-genotype XIII.1.1, while viruses from Sweden, Russia, India, and Iran from 1997 to 2011 were classified in XIII.1.2.…”

Section: Resultsmentioning

confidence: 99%

“…In other instances, new genotypes were created without applying all of the proposed criteria, or the classification was completed using a limited sequence dataset (often using partial F gene sequences) rather than using a curated dataset of all available complete NDV F gene sequences. For these reasons, there are inconsistencies in the naming and classification of some newly proposed genotypes and some sub-genotypes bear identical names while describing different and unrelated viruses (Ahmadi et al, 2016; Barman et al, 2017; Das and Kumar, 2017; Esmaelizad et al, 2017; Ganar et al, 2017; Gowthaman et al, 2018; Nath and Kumar, 2017; Servan de Almeida et al, 2013; Snoeck et al, 2013a; Xue et al, 2017a). Furthermore, with the increased surveillance efforts and the improvement of sequencing technologies, the amount of available sequences has vastly increased, adding to the already complex challenge of studying the molecular evolution of NDV and the relationships among its isolates.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus

Dimitrov

Abolnik

Afonso

et al. 2019

Infection, Genetics and Evolution

304

397

View full text Add to dashboard Cite

Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and co-workers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus

Dimitrov

Abolnik

Afonso

et al. 2019

Infection, Genetics and Evolution

304

397

View full text Add to dashboard Cite

show abstract

“…There were a total of 1654 positions in the final dataset. Evolutionary analyses were conducted using mega 6 [52]. Fig.…”

Section: Discussionmentioning

confidence: 99%

“…These viruses have historically been classified into five subgenotypes (XIII a-e) [18,20,[22][23][24]52]. However, some of these studies did not apply objective classification criteria.…”

Section: Discussionmentioning

confidence: 99%

Genetic and biological characterization of Newcastle disease viruses circulating in Bangladesh during 2010–2017: further genetic diversification of class II genotype XIII in Southcentral Asia

Nooruzzaman

Mumu

Kabiraj

et al. 2021

Journal of General Virology

View full text Add to dashboard Cite

Newcastle disease virus (NDV) is endemic in Bangladesh and is a major threat to commercial poultry operations. While complete fusion (F) genes are recommended for molecular characterization and classification of NDV isolates, heretofore, only partial F gene data have been available for Bangladeshi NDVs. To this end, we obtained the full-length F gene coding sequences of 11 representative NDVs isolated in Bangladesh between 2010 and 2017. In addition, one of the viruses (MK934289/chicken/Bangladesh/C161/2010) was used in an experimental infection of chickens to establish the viral pathotype and study gross and microscopic lesions. Phylogenetic analysis provided evidence that all studied Bangladeshi isolates belong to genotype XIII.2 of class II NDVs. Six of the viruses were isolated between 2010 and 2017 and grouped together with isolates from neighbouring India during 2013–2016. Another four Bangladeshi isolates (2010–2016) formed a separate monophyletic branch within XIII.2 and showed high nucleotide distance from the isolates from India and the other six Bangladeshi viruses within the sub-genotype; however, none of these groups fulfils all classification criteria to be named as a separate sub-genotype. The eleventh Bangladeshi virus studied here (C162) was genetically more distant from the remaining isolates. It out-grouped the viruses from sub-genotypes XIII.2.1 and XIII.2.2 and showed more than 9.5 % nucleotide distance from all genotype XIII sub-genotypes. This isolate may represent an NDV variant that is evolving independently from the other viruses in the region. The experimental infection in chickens revealed that the tested isolate (C161) is a velogenic viscerotropic virus. Massive haemorrhages, congestion and necrosis in different visceral organs, and lymphoid depletion in lymphoid tissues, typical for infection with velogenic NDV, were observed. Our findings demonstrate the endemic circulation of sub-genotype XIII.2 in Southcentral Asia and further genetic diversification of these viruses in Bangladesh and neighbouring India. This constant evolution of the viruses may lead to the establishment of new genetic groups in the region. Additional historical and prospective virus and surveillance data from the region and neighbouring countries will allow a more detailed epidemiological inference.

show abstract

“…Presence of virus was confirmed by RT-PCR using primers targeting FPCS of fusion gene (Nantha Kumar et al, 2000). Complete fusion gene was amplified using consensus primers (Gowthaman et al, 2018) and used for phylogenetic analysis and genotype determination. Services of commercial sequencing firm (Barcode Biosciences, India) were utilized for obtaining the sequence of complete fusion gene.…”

Section: Rna Extraction Cdna Synthesis Pcr and Fusion Gene Sequencingmentioning

confidence: 99%

Molecular Characterization of Velogenic Avian Avulavirus Type 1 Isolated from Apparently Healthy Emu Birds: Implications to Viral Maintenance and Spread

Deepthi¹,

Ratnamma²,

Pushpa³

et al. 2021

IJAR

View full text Add to dashboard Cite

Background: Newcastle disease caused by Avian avulavirus type 1 (AAvV-1) is one of the dreadful diseases affecting poultry and other avian species. Wild birds and several domestic birds are recognized as reservoirs of AAvV-1 and probably contribute to the epidemiology of ND in the domesticated poultry. Hence, efforts have been made to understand the virulence and genetic nature of AAvV-1 isolates obtained from apparently healthy Emu birds.Methods: This study details characterization of a velogenic Emu/5 AAvV-1 isolate obtained from an asymptomatic emu flock. Full- length fusion gene was amplified and subsequent phylogenetic analysis was performed. Experimental inoculation of 3-week old chicken with the isolate resulted in virulent ND. Expression of cytokine mRNA levels in spleen of infected chicken at different time points correlated well with the clinical picture, gross and histopathological lesions.Result: To our knowledge this is the first evidence for the role of apparently healthy emu bird acting as a reservoir of velogenic AAvV-1 of subgenotype XIII 2.2 which proved to be highly virulent to chicken. This study further highlights the role of reservoir birds in AAvV-1 transmission and the need for adopting most realistic strategies in counteracting the disease.

show abstract

Molecular phylogenetics of Newcastle disease viruses isolated from vaccinated flocks during outbreaks in Southern India reveals circulation of a novel sub‐genotype

Cited by 19 publications

References 41 publications

Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus

Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus

Genetic and biological characterization of Newcastle disease viruses circulating in Bangladesh during 2010–2017: further genetic diversification of class II genotype XIII in Southcentral Asia

Molecular Characterization of Velogenic Avian Avulavirus Type 1 Isolated from Apparently Healthy Emu Birds: Implications to Viral Maintenance and Spread

Contact Info

Product

Resources

About