Genomic and biological characterization of Newcastle disease viruses isolated from migratory mallards (Anas platyrhynchos)

Habib, Momena; Yaqub, Tahir; Nazir, Jawad; Shehzad, Wasim; Ul-Rahman, Aziz; Sohail, Tariq; Mukhtar, Nadia; Mehboob, Arsalan; Munir, Muhammad; Shabbir, Muhammad Zubair

doi:10.1007/s00705-018-3840-8

Cited by 15 publications

(18 citation statements)

References 48 publications

(38 reference statements)

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“…Despite the use of imported vaccines, AAVV-1 still remains the main poultry disease in both commercial and rural chickens flocks of Pakistan [15]. Recently, AAVV-1 s of genotype VI, VII and XIII were detected in Pakistani poultry [16][17][18][19][20][21][22][23] and genotype VII is predominant across the country. Similarly, Miller et al [24] reported that viruses of sub-genotype VIIi have replaced AAVV-1 isolates of genotype XIII in Pakistan, which were commonly isolated since 2009-2011.…”

Section: Discussionmentioning

confidence: 99%

Molecular epidemiology of respiratory viruses in commercial chicken flocks in Pakistan from 2014 through to 2016

et al. 2019

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Background Viral diseases are a matter of great concern for poultry farmers in Pakistan. Multiple common viral respiratory diseases (CVRDs) cause huge economic losses in the poultry industry. The prevalence of CVRDs in many countries, including Pakistan, is not clearly understood. Results Incidences of 5 chicken respiratory viruses: avian influenza virus (AIV), Newcastle disease virus (NDV/AAVV-1), infectious bronchitis virus (IBV), avian metapneumovirus (aMPV) and infectious laryngotracheitis virus (ILTV) were assessed on commercial Pakistani farms with respiratory problems from 2014 through to 2016. While AIV and AAVV-1 were frequently detected (16 to 17% of farms), IBV and aMPV were rarely detected (in 3 to 5% of farms) and ILTV was not detected. We characterized H9 AIV of the G1 lineage, genotype VII AAVV-1, GI-13 IBV, and type B aMPV strains with very little genetic variability in the 2-year study period. Co-infections with AIV and AAVV-1 were common and wild type AAVV-1 was detected despite the use of vaccines. Control measures to limit the virus burden in chicken flocks are discussed. Conclusions Our data shows that AIV (H9), AAVV-1, IBV and aMPV are prevalent in commercial poultry in Pakistan. Further studies are necessary to assess circulating strains, economic losses caused by infections and coinfections of these pathogens, and the costs and benefits of countermeasures. Furthermore, veterinarians and farmers should be informed of the pathogens circulating in the field and hence advised on the use of vaccines.

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Section: Discussionmentioning

confidence: 99%

Molecular epidemiology of respiratory viruses in commercial chicken flocks in Pakistan from 2014 through to 2016

et al. 2019

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“…Across Pakistan, Avian avulavirus 1 strains of genotype VI (Akhtar et al 2016;Shabbir et al 2016), VII (Shabbir et al 2012a(Shabbir et al , b, 2013(Shabbir et al , 2016Munir et al, 2012a, b;Abbas et al 2014;Farooq et al 2014;Akhtar et al 2016;Habib et al 2018;Aziz-ul-Rahman et al 2018a and XIII (Miller et al 2015;Shabbir et al 2018) (Shabbir et al 2012;Munir et al 2012a, Qamar-un-Nisa et al 2017, Akhtar et al 2017, Israel and a public zoo in Mexico (Panshin et al 2002;Miller et al 2009). Therefore, the role of wild birds as natural reservoirs in dissemination of the virus cannot be overlooked.…”

Section: Discussionmentioning

confidence: 99%

“…Class-I contains nine distinct genotypes (I-IX) of avirulent strains that share a 15198 nt long genome, while class-II contains at least eighteen distinct genotypes (I-XVIII) of high virulent, low virulent and avirulent strains that have a 15186 and/or 15192 nt long genome (Aldous et al 2003;Kim et al 2007). Based on partial sequencing of F genes (375bp between 4597-4972 nts), avualviruses of genotypes I, II, VI, VII, XIII are further divided into different sub-genotypes of both virulent and avirulent strains isolated from a wide range of avian species (Shabbir et al 2012a(Shabbir et al , b, 2013(Shabbir et al , 2016Munir et al 2012a, b;Miller et al 2015;Akhtar et al 2016;Nath and Kumar 2015;Das andKumar 2017, Xue et al 2017;Barman et al 2017;Habib et al 2018;Aziz-ul-Rahman et al 2018a.…”

Section: Introductionmentioning

confidence: 99%

“…In this regard, a vast majority of studies in Pakistan have reported the epidemiology and surveillance of ND in commercial and domestic poultry and wild susceptible avian hosts. Historically, beginning in the 1990s, these studies were limited to serosurveillance (Numan et al 2005;Aziz-ul-Rahman et al 2017); whereas in recent years, partial genome-based studies have been conducted to investigate strain genotyping (Shabbir et al 2012a(Shabbir et al , 2013Munir et al 2012b;Farooq et al 2014;Akhtar et al 2016Akhtar et al , 2017Wajid et al 2018) while few studies involved in complete genome sequencing and biologic characterization of field circulating AAvV 1 strains (Munir et al 2012a;Shabbir et al 2012bShabbir et al , 2016Shabbir et al , 2018Habib et al 2018;Aziz-ul-Rahman et al 2018a.…”

Section: Introductionmentioning

confidence: 99%

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A comparative genomic and evolutionary analysis of circulating strains of Avian avulavirus 1 in Pakistan

2019

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Newcastle disease, caused by Avian avulavirus 1 (AAvV 1), is endemic to many developing countries around the globe including Pakistan. Frequent epidemics are not uncommon even in vaccinated populations and are largely attributed to the genetic divergence of prevailing isolates and their transmission in the environment. With the strengthening of laboratory capabilities in Pakistan, a number of genetically diverse AAvV 1 strains have recently been isolated and individually characterized in comparison with isolates reported elsewhere in the world. However, there lacks sufficient comparative genomic and phylogenomic analyses of field circulating strains that can elucidate the evolutionary dynamics over a period of time. Herein, we enriched the whole genome sequences of AAvV reported so far (n= 35) from Pakistan and performed comparative genomic, phylogenetic and evolutionary analyses. Based on these analyses, we found only isolates belonging to genotypes VI, VII and XIII of AAvV 1 in a wide range of avian and human hosts. Comparative phylogeny revealed the concurrent circulation of avualviruses representing different sub-genotypes such as VIg, VIm, VIIa, VIIb, VIIe, VIIf, VIIi, XIIIb and XIIId. We found that that isolates of genotype VII were more closely associated with viruses of genotype XIII than genotype VI. An inter-genotype comparative residue analysis revealed a few substitutions in structurally and functionally important motifs. Putative recombination events were reported for only one of the captive-wild bird (pheasant)origin isolates. The viruses of genotype VII had high genetic diversity as compared to isolates from genotypes VI and XIII and, therefore, have more potential to evolve over time. Taken together, the current study provides an insight into the genetic diversity and evolutionary dynamics of AAvV 1 circulating in Pakistan. Such findings are expected to facilitate better intervention strategies for the prevention and control of ND in disease-endemic countries across the globe particularly Pakistan.

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“…Waterfowl, the natural reservoir of NDVs, has the potential to spread the virus in the environment and within their susceptible hosts. It results in frequent ND outbreaks and subsequent economic losses [8][9][10]. Class I NDVs were originally recovered from both domestic and wild birds sampled in North America and Eurasia since at least the 1970s [6,11,12].…”

Section: Introductionmentioning

confidence: 99%

Genetic evolution of class I Newcastle disease virus from poultry at live bird markets in Eastern China

Lü

Wang

Sun

et al. 2020

Preprint

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Background: Live bird markets (LBMs) serve as a natural reservoir for class I Newcastle disease virus (NDV) and play an important role in viral evolution and spread. LBMs and commercial farms are the main sources of daily poultry products. However, limited studies are available for the class I NDV circulating at LBMs and commercial farms. In this study, significant progress has been made in sample detection and genetic analysis at LBMs and commercial farms in Eastern China.Methods: A long-term epidemiological investigation at LBMs and commercial farms in Eastern China was conducted. We sequentially conducted the collection of samples, virus isolation, RNA extraction, RT-PCR, and phylogenetic analysis. We also analyzed class I NDVs deposited in NCBI during 2002–2018 from China in terms of the host, genotype, time, and functional domains.Results: Here we report that class I NDVs continue to circulate in LBMs. Class I NDVs were detected at a high prevalence in chickens (23/26) but were seldom detected in waterfowl (3/26) at LBMs. In contrast, class I NDVs were rarely detected in commercial chickens but were present in commercial waterfowl at a certain frequency before they were brought to the LBMs. This observation suggests that the mixture of poultry and the conventional housing at LBMs cause the spread of class I NDVs. Sequence analysis of Class I NDV genomes deposited in NCBI during 2002–2018 from China revealed a high prevalence of class I NDVs in terrestrial birds (82.7%), which was much higher than in water birds (17.3%). In addition, we found that the class I NDVs predominantly belonged to the sub-genotype 3c and rarely evolved into a new sub-genotype such as the 3d. Furthermore, the epidemic sub-genotype 3c seems to be under ongoing evolution.Conclusions: Our study provides evidence that the traditional feeding mode at LBMs causes the spread of class I NDVs and poses a great risk of NDV epidemics in the poultry industry in Eastern China. The sub-genotype 3c is circulating at LBMs and currently the terrestrial bird is the predominant host of class I NDVs.

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Genomic and biological characterization of Newcastle disease viruses isolated from migratory mallards (Anas platyrhynchos)

Cited by 15 publications

References 48 publications

Molecular epidemiology of respiratory viruses in commercial chicken flocks in Pakistan from 2014 through to 2016

Molecular epidemiology of respiratory viruses in commercial chicken flocks in Pakistan from 2014 through to 2016

A comparative genomic and evolutionary analysis of circulating strains of Avian avulavirus 1 in Pakistan

Genetic evolution of class I Newcastle disease virus from poultry at live bird markets in Eastern China

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