Phylogenetic assessment reveals continuous evolution and circulation of pigeon-derived virulent avian avulaviruses 1 in Eastern Europe, Asia, and Africa

Sabra, Mahmoud; Dimitrov, Kiril M.; Goraichuk, Iryna V.; Wajid, Abdul; Sharma, Poonam; Williams-Coplin, Dawn; Basharat, Asma; Rehmani, Shafqat Fatima; Muzyka, Denys; Miller, Patti J.; Afonso, Claudio L.

doi:10.1186/s12917-017-1211-4

Cited by 50 publications

(51 citation statements)

References 60 publications

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“…While both types of viruses infected chickens and were actively shed, the pigeon-origin virus did not cause mortality, consistent with previous studies [38]. Despite that many PPMV-1 are characterized as being of low or moderate pathogenicity for chickens, their potential to cause disease in poultry should not be underestimated [24,39]. Indeed, it has been reported that only several point mutations are sufficient to increase the pathogenicity of PPMV-1 in chickens [35,40].…”

Section: Discussionsupporting

confidence: 88%

“…[12,44]. There have been reports of PPMV-1 being maintained in healthy captive [24,44] or wild pigeons [23].…”

Section: Discussionmentioning

confidence: 99%

“…For the studied isolates, total RNA was isolated from the allantoic fluid using the QIAamp RNA viral mini kit (Qiagen, Hilden, North Rhine-Westphalia, Germany) and processed by next-generation sequencing using KAPA Stranded RNA-Seq kit (KAPA Biosystems, USA),as previously described [23,24]. All NGS libraries underwent equimolar dilution and were pooled.…”

Section: Rna Extraction Next-generation Sequencing (Ngs) Library Prementioning

confidence: 99%

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Complete Genome Sequencing, Molecular Epidemiological, and Pathogenicity Analysis of Pigeon Paramyxoviruses Type 1 Isolated in Guangxi, China during 2012–2018

Dimitrov³

et al. 2020

Viruses

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Newcastle disease is an important poultry disease that also affects Columbiform birds. The viruses adapted to pigeons and doves are referred to as pigeon paramyxoviruses 1 (PPMV-1). PPMV-1 are frequently isolated from pigeons worldwide and have the potential to cause disease in chickens. The complete genomes of 18 PPMV-1 isolated in China during 2012–2018 were sequenced by next-generation sequencing (NGS). Comprehensive phylogenetic analyses showed that five of the viruses belong to sub-genotype VI1.2.1.1.2.1 and 13 isolates belong to sub-genotype VI.2.1.1.2.2. The results demonstrate that these sub-genotypes have been predominant in China during the last decade. The viruses of these sub-genotypes have been independently maintained and continuously evolved for over 20 years, and differ significantly from those causing outbreaks worldwide during the 1980s to 2010s. The viral reservoir remains unknown and possibilities of the viruses being maintained in both pigeon farms and wild bird populations are viable. In vivo characterization of the isolates’ pathogenicity estimated mean death times between 62 and 114 h and intracerebral pathogenicity indices between 0.00 and 0.63. Cross-reactivity testing showed minor antigenic differences between the studied viruses and the genotype II LaSota vaccine. These data will facilitate PPMV-1 epidemiology studies, vaccine development, and control of Newcastle disease in pigeons and poultry.

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Section: Discussionsupporting

confidence: 88%

“…[12,44]. There have been reports of PPMV-1 being maintained in healthy captive [24,44] or wild pigeons [23].…”

Section: Discussionmentioning

confidence: 99%

Section: Rna Extraction Next-generation Sequencing (Ngs) Library Prementioning

confidence: 99%

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Complete Genome Sequencing, Molecular Epidemiological, and Pathogenicity Analysis of Pigeon Paramyxoviruses Type 1 Isolated in Guangxi, China during 2012–2018

Dimitrov³

et al. 2020

Viruses

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“…Currently, there are at least three NDV genotypes circulating in Egypt: besides vaccine type genotype 2.II virus, virulent genotype 2.VIb and 2.VIIb are present. Genotype 2.VIb was isolated mainly from infected pigeons and regarded as pigeon paramyxovirus (PPMV) (Rohaim et al, 2016;Sabra et al, 2017). Genotype 2.VIIb, in contrast, is relevant for poultry, with numerous outbreaks of ND in all chicken production sectors.…”

Section: Original Articlementioning

confidence: 99%

Investigation of suspected Newcastle disease (ND) outbreaks in Egypt uncovers a high virus velogenic ND virus burden in small-scale holdings and the presence of multiple pathogens

et al. 2019

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Highly contagious Newcastle disease (ND) is associated with devastating outbreaks with highly variable clinical signs among gallinaceous birds. In this study we aimed to verify clinical ND suspicions in poultry holdings in Egypt suffering from respiratory distress and elevated mortality, comparing two groups of ND-vaccinated poultry holdings in three governorates. Besides testing for Newcastle disease virus (NDV), samples were screened for infectious bronchitis virus (IBV) and avian influenza virus (AIV) by RT-qPCR as well as by non-directed cell-culture approach on LMH-cells. Virulent NDV was confirmed only in group A (n = 16) comprising small-scale holdings. Phylogenetic analysis of the fusion protein gene of 11 NDVpositive samples obtained from this group assigned all viruses to genotype 2.VIIb and point to four different virus populations that were circulating at the same time in one governorate, indicating independent epidemiological events. In group B, comprising large commercial broiler farms (n = 10), virulent NDV was not present, although in six farms NDV vaccine-type virus (genotype 2.II) was detected. Besides, in both groups, co-infections by IBV (n = 10), AIV H9 (n = 3) and/or avian reovirus (ARV) (n = 5) and avian astrovirus (AastVs) (n = 1) could be identified. Taken together, the study confirmed clinical ND suspicion in small scale holdings, pointing to inefficient vaccination practices in this group A. However, it also highlighted that, even in an endemic situation like ND in Egypt, in cases of suspected ND vaccine failure, clinical ND suspicion has to be verified by pathotype-specific diagnostic tests. RESEARCH HIGHLIGHTS. Velogenic NDV circulates in small-scale poultry holdings in Egypt. . Viral transmission occurred among neighbouring farms and over long distances. . Co-infections with multiple pathogens were identified. . Pathotype specific diagnostic tests are essential to verify ND suspicions. ARTICLE HISTORY

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“…In Egypt, ND remains one of the primary poultry diseases in both commercial and backyard chickens since recorded in 1948, despite vaccination. As previously reported, genotype VII has been responsible for ND outbreaks in the commercial chickens; whereas genotype VI has been isolated from diseased pigeons since early 1981 in Egypt [23,32]. Continuous active surveillance and genetic analysis of NDVs isolated from vaccinated flocks will provide insights into the current situation.…”

Section: Introductionmentioning

confidence: 90%

Molecular characterization of full genome sequences of Newcastle disease viruses circulating among vaccinated chickens in Egypt during 2011–2013

Tran

Sultan

Osman

et al. 2020

The Journal of Veterinary Medical Science

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Although intensive vaccination programs have been implemented, Newcastle disease (ND) outbreaks, accompanied by severe economic losses, are still reported in Egypt. The genetic characterization of ND virus (NDV) strains isolated from ND-vaccinated chicken flocks provides essential information for improving ND control strategies. Therefore, here, 38 NDV strains were isolated and identified from outbreaks among vaccinated flocks of broiler chickens located in the provinces of Qena, Luxor, and Aswan of Upper Egypt during 2011-2013. The investigated broiler chicken flocks (aged 28 to 40 days) had high mortality rates of up to 80%. All NDV isolates were genetically analyzed using next-generation DNA sequencing. From these isolates, 10 representative NDV strains were selected for further genetic analyses. Phylogenetic analysis of full-length coding genes revealed that the Egyptian NDV isolates belonged to a single sub-genotype, VII.1.1. These isolates were phylogenetically distant from the vaccine strains, including La Sota or Clone 30 (genotype II), which have been commonly used to vaccinate chicken flocks. Amino acid substitution K78R was observed in the neutralizing epitopes of the F proteins; whereas several mutations were found in the neutralizing epitopes of the hemagglutinin-neuraminidase proteins, notably, E347K. Overall, our results suggested that the occurrence of neutralizing epitope variants may be one of potential reasons for ND outbreaks. Further studies are needed to determine the protective effect of current vaccines against circulating virulent NDV strains.

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Phylogenetic assessment reveals continuous evolution and circulation of pigeon-derived virulent avian avulaviruses 1 in Eastern Europe, Asia, and Africa

Cited by 50 publications

References 60 publications

Complete Genome Sequencing, Molecular Epidemiological, and Pathogenicity Analysis of Pigeon Paramyxoviruses Type 1 Isolated in Guangxi, China during 2012–2018

Complete Genome Sequencing, Molecular Epidemiological, and Pathogenicity Analysis of Pigeon Paramyxoviruses Type 1 Isolated in Guangxi, China during 2012–2018

Investigation of suspected Newcastle disease (ND) outbreaks in Egypt uncovers a high virus velogenic ND virus burden in small-scale holdings and the presence of multiple pathogens

Molecular characterization of full genome sequences of Newcastle disease viruses circulating among vaccinated chickens in Egypt during 2011–2013

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