RNA-dependent RNA polymerase gene analysis of worldwide Newcastle disease virus isolates representing different virulence types and their phylogenetic relationship with other members of the paramyxoviridae

Genetic characterization and distribution of the virus in chicken embryo tissues infected with Newcastle disease virus isolated from commercial and native chickens in Indonesia

Background and Aim:

Newcastle disease (ND) is a viral infectious disease that affects commercial and native chickens, resulting in economic losses to the poultry industry. This study aimed to examine the viral strains circulating in commercial and native chickens by genetic characterization and observe the distribution of Newcastle disease virus (NDV) in chicken embryonic tissue.

Materials and Methods:

ND was detected using a quantitative reverse transcription-polymerase chain reaction. Genetic characterization of the fusion (F) and hemagglutinin-neuraminidase (HN) genes from the eight NDVs was performed using specific primers. The sequence was compared with that of other NDVs from GenBank and analyzed using the MEGA-X software. The distribution of NDV in chicken embryos was analyzed based on lesions and the immunopositivity in immunohistochemistry staining.

Results:

Based on F gene characterization, velogenic NDV strains circulating in commercial and native chickens that showed varying clinical symptoms belonged to genotype VII.2. Lentogenic strains found in chickens without clinical symptoms were grouped into genotype II (unvaccinated native chickens) and genotype I (vaccinated commercial chickens). Amino acid variations in the HN gene, namely, the neutralization epitope and antigenic sites at positions 263 and 494, respectively, occurred in lentogenic strains. The NDV reaches the digestive and respiratory organs, but in lentogenic NDV does not cause significant damage, and hence embryo death does not occur.

Conclusion:

This study showed that velogenic and lentogenic NDV strains circulated in both commercial and native chickens with varying genotypes. The virus was distributed in almost all organs, especially digestive and respiratory. Organ damage in lentogenic infection is not as severe as in velogenic NDV. Further research is needed to observe the distribution of NDV with varying pathogenicity in chickens.

A comparative phylogenomic analysis of avian avulavirus 1 isolated from non-avian hosts: conquering new frontiers of zoonotic potential among species

A number of avian avulavirus 1 (AAvV 1) isolates have been reported from avian and non-avian hosts worldwide with varying clinical consequences. In this regard, robust surveillance coupled with advanced diagnostics, genomic analysis, and disease modelling has provided insight into the molecular epidemiology and evolution of this virus. The genomic and evolutionary characteristics of AAvV 1 isolates originating from avian hosts have been well studied, but those originating from non-avian hosts have not. Here, we report a comparative genomic and evolutionary analysis of so-far reported AAvV 1 isolates originating from hosts other than avian species (humans, mink and swine). Phylogenetic analysis showed that AAvV 1 isolates clustered in five distinct genotypes (I, II, VI, VII and XIII). Further analysis revealed clustering of isolates into clades distant enough to be considered distinct subgenotypes, along with a few substitutions in several significant motifs. Although further investigation is needed, the clustering of AAvV 1 strains isolated from non-avian hosts into novel subgenotypes and the presence of substitutions in important structural and biological motifs suggest that this virus can adapt to novel hosts and therefore could have zoonotic potential.

Urbanization and the dynamics of RNA viruses in Mallards (Anas platyrhynchos)

Urbanization is intensifying worldwide, and affects the epidemiology of infectious diseases. However, the effect of urbanization on natural host-pathogen systems remains poorly understood. Urban ducks occupy an interesting niche in that they directly interact with both humans and wild migratory birds, and either directly or indirectly with food production birds. Here we have collected samples from Mallards (Anas platyrhynchos) residing in a pond in central Uppsala, Sweden, from January 2013 to January 2014. This artificial pond is kept ice-free during the winter months, and is a popular location where the ducks are fed, resulting in a resident population of ducks year-round. Nine hundred and seventy seven (977) fecal samples were screened for RNA viruses including: influenza A virus (IAV), avian paramyxovirus 1, avian coronavirus (CoV), and avian astrovirus (AstroV). This intra-annual dataset illustrates that these RNA viruses exhibit similar annual patterns to IAV, suggesting similar ecological factors are at play. Furthermore, in comparison to wild ducks, autumnal prevalence of IAV and CoV are lower in this urban population. We also demonstrate that AstroV might be a larger burden to urban ducks than IAV, and should be better assessed to demonstrate the degree to which wild birds contribute to the epidemiology of these viruses. The presence of economically relevant viruses in urban Mallards highlights the importance of elucidating the ecology of wildlife pathogens in urban environments, which will become increasingly important for managing disease risks to wildlife, food production animals, and humans.

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Influenza virus, coronavirus, paramyxovirus, astrovirus detected in urban Mallards

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Viruses share intra-annual dynamics, with autumnal prevalence peak

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Avian astrovirus had the highest prevalence in urban Mallards.

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Prevalence of influenza and coronavirus lower in urban versus to migrating Mallard

Constraints on the Genetic and Antigenic Variability of Measles Virus

Antigenic drift and genetic variation are significantly constrained in measles virus (MeV). Genetic stability of MeV is exceptionally high, both in the lab and in the field, and few regions of the genome allow for rapid genetic change. The regions of the genome that are more tolerant of mutations (i.e., the untranslated regions and certain domains within the N, C, V, P, and M proteins) indicate genetic plasticity or structural flexibility in the encoded proteins. Our analysis reveals that strong constraints in the envelope proteins (F and H) allow for a single serotype despite known antigenic differences among its 24 genotypes. This review describes some of the many variables that limit the evolutionary rate of MeV. The high genomic stability of MeV appears to be a shared property of the Paramyxovirinae, suggesting a common mechanism that biologically restricts the rate of mutation.

Genetic characterization and evolutionary analysis of Newcastle disease virus isolated from domestic duck in South Korea

Domestic ducks are considered a potential reservoir of Newcastle disease virus. In the study, a Newcastle disease virus (NDV) isolated from a domestic duck during surveillance in South Korea was characterized. The complete genome of the NDV isolate was sequenced, and the phylogenetic relationship to reference strains was studied. Phylogenetic analysis revealed that the strain clustered in genotype I of Class II ND viruses, has highly phylogenetic similarity to NDV strains isolated from waterfowl in China, but was distant from the viruses isolated in chickens and vaccine strains used in South Korea. Pathogenicity experiment in chickens revealed it to be a lentogenic virus. The deduced amino acid sequence of the cleavage site of the fusion (F) protein confirmed that the isolate contained the avirulent motif (112)GKQGRL(117) at the cleavage site and caused no apparent disease in chickens and ducks. With phylogeographic analysis based on fusion gene, we estimate the origin of an ancestral virus of the isolate and its sister strain located in China around 1998. It highlights the need of continuous surveillance to enhance current understanding of the molecular epidemiology and evolution of the pathogenic strains.

Temporal dynamics, diversity, and interplay in three components of the virodiversity of a Mallard population: influenza A virus, avian paramyxovirus and avian coronavirus

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In the autumn of 2011, 3029 samples collected from 144 Mallards.

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A high prevalence of influenza A with 27 different HA/NA subtype combinations.

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A bimodal seasonal prevalence curve, up to 12%, of gammacoronavirus.

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An increased coronavirus prevalence given birds are coinfected with influenza A.

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Low prevalence and diversity of avian paramyxovirus type 1.

Multiple infections, or simultaneous infection of a host with multiple parasites, are the rule rather than the exception. Interactions between co-occurring pathogens in a population may be mutualistic, competitive or facilitative. For some pathogen combinations, these interrelated effects will have epidemiological consequences; however this is as yet poorly incorporated into practical disease ecology. For example, screening of Mallards for influenza A viruses (IAV) have repeatedly revealed high prevalence and large subtype diversity in the Northern Hemisphere. Other studies have identified avian paramyxovirus type 1 (APMV-1) and coronaviruses (CoVs) in Mallards, but without making inferences on the larger viral assemblage. In this study we followed 144 wild Mallards across an autumn season in a natural stopover site and constructed infection histories of IAV, APMV-1 and CoV. There was a high prevalence of IAV, comprising of 27 subtype combinations, while APMV-1 had a comparatively low prevalence (with a peak of 2%) and limited strain variation, similar to previous findings. Avian CoVs were common, with prevalence up to 12%, and sequence analysis identified different putative genetic lineages. An investigation of the dynamics of co-infections revealed a synergistic effect between CoV and IAV, whereby CoV prevalence was higher given that the birds were co-infected with IAV. There were no interactive effects between IAV and APMV-1. Disease dynamics are the result of an interplay between parasites, host immune responses, and resources; and is imperative that we begin to include all factors to better understand infectious disease risk.

Development of strand-specific real-time RT-PCR to distinguish viral RNAs during Newcastle disease virus infection

Newcastle disease virus (NDV) causes large losses in the global fowl industry. To better understand NDV replication and transcription cycle, quantitative detection methods for distinguishing NDV genomic RNA (gRNA), antigenomic RNA (cRNA), and messenger RNA (mRNA) in NDV-infected cells are indispensible. Three reverse transcription primers were designed to specifically target the nucleoprotein (NP) region of gRNA, cRNA, and NP mRNA, and a corresponding real-time RT-PCR assay was developed to simultaneously quantify the three types of RNAs in NDV-infected cells. This method showed very good specificity, sensitivity, and reproducibility. The detection range of the assay was between 5.5 × 10² and 1.1 × 10⁹ copies/μL of the target gene. These methods were applied to investigate the dynamics of the gRNA, cRNA, and mRNA synthesis in NDV La Sota infected DF-1 cells. The results showed that the copy numbers of viral gRNA, cRNA, and NP mRNA all exponentially increased in the beginning. The viral RNA copy number then plateaued at 10'h postinfection and gradually decreased from 16 h postinfection. No synthesis priority was observed between replication (gRNA and cRNA amounts) and transcription (mRNA amounts) during NDV infection. However, the cRNA accumulated more rapidly than gRNA, as the cRNA copy number was three- to tenfold higher than gRNA starting from 2 h postinfection. Conclusion. A real-time RT-PCR for absolute quantitation of specific viral RNA fragments in NDV-infected cells was developed for the first time. The development of this assay will be helpful for further studies on the pathogenesis and control strategies of NDV.

Pigeon paramyxovirus type 1 variants with polybasic F protein cleavage site but strikingly different pathogenicity

Newcastle disease viruses (NDV) isolated from pigeons (pigeon paramyxovirus type 1; PPMV-1) are mostly of mesogenic pathotype and characterized by a polybasic amino acid sequence motif at the fusion protein (F) cleavage site. This feature also applies to isolate R75/98 from Germany. Its genome consists of 15,192 nucleotides and it specifies an intracerebral pathogenicity index (ICPI) of 1.1, as is typical for mesogenic NDV. Recombinant R75/98 (rR75/98) derived by reverse genetics also possesses a polybasic F protein cleavage site but exhibits ICPI of 0.28, indicating a lentogenic virus. While ten virus passages of rR75/98 on embryonated chicken eggs did not result in any alteration of virus characteristics, virus which had been re-isolated from the brain of an intracerebrally inoculated chicken showed an increase in virulence, characterized by an ICPI of 0.93. Comparison of whole genome sequences of rR75/98 and re-isolated rR75/98 (RrR75/98) demonstrated only two amino acid differences, one in the F protein (N472 K) and one in the polymerase protein (K2168R). This result indicates that only very few amino acid alterations are sufficient to modulate virus virulence in the presence of a polybasic amino acid sequence at the proteolytic F protein cleavage site.

Molecular and phylogenetic characterization based on the complete genome of a virulent pathotype of Newcastle disease virus isolated in the 1970s in Brazil

Newcastle disease (ND) is caused by the avian paramyxovirus type 1 (APMV-1) or Newcastle disease virus (NDV) that comprises a diverse group of viruses with a single-stranded, negative-sense RNA genome. ND is one of the most important diseases of chickens, because it severely affects poultry production worldwide. In the 1970s, outbreaks of virulent ND were recorded in Brazil, and the strain APMV-1/Chicken/Brazil/SJM/75 (SJM) of NDV was isolated. This strain was characterized as highly pathogenic for chickens but not pathogenic for other bird species. Here we present the complete genome of NDV strain SJM and investigate the phylogenetic relationships of this virus with other NDV strains in terms of genome and proteins composition, as well as characterizing its evolution process. The NDV strain SJM is categorized as a velogenic virus and the complete genome is 15,192 nucleotides in length, consisting of six genes in the order 3'-NP-P-M-F-HN-L-5'. The presence of the major pathogenic determinant of NDV strains ((112)R-R-Q-K-R↓F(117)) was identified in the Fusion protein of the NDV strain SJM. In addition, phylogenetic analysis classified the NDV strain SJM as a member of class II, genotype V, and indicates that this virus help us in the understanding of the evolutionary process of strains belonging to this genotype. This study contributes to the growing interest involving the characterization of NDV isolates to improve our current understanding about the epidemiology, surveillance and evolution of the pathogenic strains.

Molecular characterization and phylogenetic study of velogenic Newcastle disease virus isolates in Iran

The pathogenicity and genetic characterizations of six Newcastle disease virus (NDV) isolates obtained from chicken farms in six different regions in Iran were carried out using conventional and molecular techniques. Based on the pathogenicity indices (MDT, ICPI, and IVPI), all of these isolates were found to be velogenic (highly virulent) strains. A sequence analysis of the full-length mRNA encoding the fusion glycoprotein precursor (F0) of the NDV's fusion proteins F1 and F2 in these six isolates showed the presence of point mutations in form of nucleic acid substitutions at positions 82((C→T)), 83((T→C)), 736((A→G)), and 1,633((G→A)). However, the nucleic acid residues at positions 330-347 of the precursor F0 gene, corresponding to the cleavage site of the F0 protein, were found to have remained conserved among the six NDV isolates. A phylogenetic comparison between the six Iranian isolates and the NDVs whose F0 gene sequences were previously deposited in GenBank Database showed that all of the newly characterized Iranian NDV isolates belonged to genotype VII.

Complete genome sequencing and analysis of an anti-tumor Newcastle disease virus strain

HBNU/LSRC/F3, a Newcastle disease virus (NDV) strain stored in our lab, exhibited an anti-tumor ability in our previous studies. Nonetheless, very little is known about its genome sequence, which is vital for further study. Here, the complete HBNU/LSRC/F3 genome was fully sequenced and compared with other NDV sequences. Its genome contained 15,192 nucleotides (nt) consisting of two termini and six genes in the following order: 3'-Le-NP-P-M-F-HN-L-Tr-5'. Phylogenetic analysis indicated that this NDV strain belonged to the Class II genotype IX group. A multibasic amino acid (aa) sequence was found at the cleavage site ((112)RRQRR↓F(117)) within the fusion (F) protein, and a 6 nt insertion was present in the 5' non-coding region of the NP gene. The whole genome sequence was highly similar to other genotype IX NDV genomes reported in China. Overall, this study provides insight into the sequence characteristics of genotype IX NDVs, which will be useful for subsequent investigations.

Neurological lesions in chickens experimentally infected with virulent Newcastle disease virus isolates

Distribution, character, and severity of lesions were evaluated in tissues from the central nervous system of chickens inoculated with 10 different Newcastle disease virus (NDV) isolates: CA 1083, Korea 97-147, Australia (all velogenic viscerotropic), Texas GB and Turkey North Dakota (both velogenic neurotropic), Nevada cormorant, Anhinga and Roakin (all mesogenic), and B1 and QV4 (lentogenic). Tissues for the present study included archived formalin-fixed, paraffin-embedded brain (all strains) plus spinal cord (two strains). Encephalitis was observed in all velogenic viscerotropic and velogenic neurotropic strains, and in some mesogenic strains. In general, the encephalitic lesions began at 5 days post infection, with more severe lesions occurring around 10 days post infection. At this time point, especially in the grey matter of the brain, cerebellum and spinal cord, there were neuronal necrosis, neuronal phagocytosis, and clusters of cells with microglial morphology. Axonal degeneration and demyelination was also observed. Immunohistochemistry (IHC) for viral nucleoprotein confirmed the presence of virus. In the areas of encephalomyelitis, IHC for CD3 revealed that many of the inflammatory cells were T lymphocytes. IHC using an antibody for glial fibrillar acid protein showed reactive astrogliosis, which was most pronounced at the later time points.

Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early-genotype phylogenetic position and recent-genotype genome size

BACKGROUND

Six nucleotide (nt) insertion in the 5'-noncoding region (NCR) of the nucleoprotein (NP) gene of Newcaslte disease virus (NDV) is considered to be a genetic marker for recent genotypes of NDV, which emerged after 1960. However, F48-like NDVs from China, identified a 6-nt insert in the NP gene, have been previously classified into genotype III or genotype IX.

RESULTS

In order to clarify their phylogenetic position and explore the origin of NDVs with the 6-nt insert and its significance in NDV evolution, we determined the entire genome sequences of five F48-like viruses isolated in China between 1946 and 2002 by RT-PCR amplification of overlapping fragments of full-length genome and rapid amplification of cDNA ends. All the five NDV isolates shared the same genome size of 15,192-nt with the recent genotype V-VIII viruses whereas they had the highest homology with early genotype III and IV isolates.

CONCLUSIONS

The unique characteristic of the genome size and phylogenetic position of F48-like viruses warrants placing them in a separate geno-group, genotype IX. Results in this study also suggest that genotype IX viruses most likely originate from a genotype III virus by insertion of a 6-nt motif in the 5'-NCR of the NP gene which had occurred as early as in 1940 s, and might be the common origin of genotype V-VIII viruses.

Passaging of a Newcastle disease virus pigeon variant in chickens results in selection of viruses with mutations in the polymerase complex enhancing virus replication and virulence

Some Newcastle disease virus (NDV) variants isolated from pigeons (pigeon paramyxovirus type 1; PPMV-1) do not show their full virulence potential for domestic chickens but may become virulent upon spread in these animals. In this study we examined the molecular changes responsible for this gain of virulence by passaging a low-pathogenic PPMV-1 isolate in chickens. Complete genome sequencing of virus obtained after 1, 3 and 5 passages showed the increase in virulence was not accompanied by changes in the fusion protein--a well known virulence determinant of NDV--but by mutations in the L and P replication proteins. The effect of these mutations on virulence was confirmed by means of reverse genetics using an infectious cDNA clone. Acquisition of three amino acid mutations, two in the L protein and one in the P protein, significantly increased virulence as determined by intracerebral pathogenicity index tests in day-old chickens. The mutations enhanced virus replication in vitro and in vivo and increased the plaque size in infected cell culture monolayers. Furthermore, they increased the activity of the viral replication complex as determined by an in vitro minigenome replication assay. Our data demonstrate that PPMV-1 replication in chickens results in mutations in the polymerase complex rather than the viral fusion protein, and that the virulence level of pigeon paramyxoviruses is directly related to the activity of the viral replication complex.

Molecular characterization of partial fusion gene and C-terminus extension length of haemagglutinin-neuraminidase gene of recently isolated Newcastle disease virus isolates in Malaysia

Background

Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a highly contagious disease of birds and has been one of the major causes of economic losses in the poultry industry. Despite routine vaccination programs, sporadic cases have occasionally occurred in the country and remain a constant threat to commercial poultry. Hence, the present study was aimed to characterize NDV isolates obtained from clinical cases in various locations of Malaysia between 2004 and 2007 based on sequence and phylogenetic analysis of partial F gene and C-terminus extension length of HN gene.

Results

The coding region of eleven NDV isolates fusion (F) gene and carboxyl terminal region of haemagglutinin-neuraminidase (HN) gene including extensions were amplified by reverse transcriptase PCR and directly sequenced. All the isolates have shown to have non-synonymous to synonymous base substitution rate ranging between 0.081 - 0.264 demonstrating presence of negative selection. Analysis based on F gene showed the characterized isolates possess three different types of protease cleavage site motifs; namely ¹¹²RRQKRF¹¹⁷, ¹¹²RRRKRF¹¹⁷ and ¹¹²GRQGRL¹¹⁷ and appear to show maximum identities with isolates in the region such as cockatoo/14698/90 (Indonesia), Ch/2000 (China), local isolate AF2240 indicating the high similarity of isolates circulating in the South East Asian countries. Meanwhile, one of the isolates resembles commonly used lentogenic vaccine strains. On further characterization of the HN gene, Malaysian isolates had C-terminus extensions of 0, 6 and 11 amino acids. Analysis of the phylogenetic tree revealed that the existence of three genetic groups; namely, genotype II, VII and VIII.

Conclusions

The study concluded that the occurrence of three types of NDV genotypes and presence of varied carboxyl terminus extension lengths among Malaysian isolates incriminated for sporadic cases.

Complete genome sequence of highly virulent neurotropic Newcastle disease virus strain Texas GB

Newcastle disease virus (NDV) strain Texas GB is a highly virulent neurotropic virus that is used as a standard vaccine challenge virus in the U.S. In this study, the complete genome sequence of strain Texas GB was determined and compared with the complete genome sequences of other NDV strains. The genome is 15,186 nucleotides (nt) long and consists of six genes in the order of 3'leader-N-P-M-F-HN-L-5'trailer. The genome contains a 55-nt leader sequence at the 3' end and a 114-nt trailer sequence at the 5' end. The intergenic sequences are 2, 1, 1, 31, and 47 nt between N/P, P/M, M/F, F/HN, and HN/L genes, respectively. The putative cleavage site of fusion protein showed amino acid sequence of R-R-Q-K-R downward arrow F in position 112 to 117, which corresponds to those of virulent NDV strains. The phylogenetic analysis showed that strain Texas GB is closely related to the neurovirulent mesogenic strain Beaudette C (BC) and to NDV viruses isolated in China and Egypt than to other strains of NDV.

Phylogenetic and pathogenic analysis of Newcastle disease virus isolated from house sparrow (Passer domesticus) living around poultry farm in southern China

House sparrow (Passer domesticus) is one of the most widely distributed wild birds in China. Five Newcastle disease virus (NDV) strains were isolated from house sparrows living around the poultry farms in southern China. These isolates were characterized by pathogenic assays and phylogenetic analysis. The results showed that all NDV isolates except one were velogenic and virulent for chickens. These four virulent strains for chickens possess the amino acid sequence (112)R/K-R-Q-K/R-R-F(117) in the F(0) cleavage site which is typical of velogenic NDV. Phylogenetic analysis indicated that these isolates belong to genotype VII and were closely related to the strains which were isolated from NDV outbreaks in chickens since 2000. One isolate of NDV from house sparrow belong to genotype II and was proved to be vaccine strain (Chicken/U.S./LaSota/46). The result of this study proved that house sparrow can carry the virulent NDV strains and the same genotype of viruses that are circulating in poultry are existing in house sparrows living around poultry farm in southern China.

Selection characterization on overlapping reading frame of multiple-protein-encoding P gene in Newcastle disease virus

The aim of this study was to characterize the molecular evolution of P and V protein genes of the Newcastle disease virus (NDV). The P gene sequences of 55 NDV isolates, representing different chronological and geographic origins, were obtained from GenBank. In this paper, the evolution of the specific regions of the NDV P gene, encoding the P and V proteins, was analyzed. The nucleotides from the shared P/V region encoded the co-amino terminus of the two proteins, while the P-V/V-P region was respectively encoded by the nucleotides within the P ORF or the V ORF in the common sequence (after the mRNA editing site). As well, the P-cut region exclusively encoded the P protein. Finally, the P-V and V-P regions were further broken down into P1 and P2 fragments with the corresponding V1 and V2 fragments. In the P gene, the P-cut portion corresponding to the C-terminal of the P protein was the most highly conserved, while the P-V region was the most variable. This was interpreted as a lower constraint for function in the common sequence than in the unique P sequence that is known to contain an important function. Interestingly, in the common P-V/V-P function, variability of V1 was compensated by a higher conservation of the corresponding P1, and conversely for the P2/V2, which suggested that the flexibility of one ORF with less function served the purpose of allowing positive selection in the other overlapping ORF that exhibited more function.

Reassessing conflicting evolutionary histories of the Paramyxoviridae and the origins of respiroviruses with Bayesian multigene phylogenies

The evolution of paramyxoviruses is still poorly understood since past phylogenetic studies have revealed conflicting evolutionary signals among genes, and used varying methods and datasets. Using Bayesian phylogenetic analysis of full length single and concatenated sequences for the 6 genes shared among paramyxovirus genera, we reassess the ambiguous evolutionary relationships within the family, and examine causes of varying phylogenetic signals among different genes. Relative to a pneumovirus outgroup, the concatenated gene phylogeny, splits the Paramyxovirinae into two lineages, one comprising the avulaviruses and rubulaviruses, and a second containing the respiroviruses basal to the henipaviruses, and morbilliviruses. Phylogenies for the matrix (M), RNA dependent RNA polymerase (L) and the fusion (F) glycoprotein genes, are concordant with the topology from the concatenated dataset. In phylogenies derived from the nucleocapsid (N) and phosphoprotein (P) genes, the respiroviruses form the most basal genus of the Paramyxovirinae subfamily, with the avulaviruses and rubulaviruses in one lineage, and the henipaviruses, and morbilliviruses in a second. The phylogeny of the hemagglutinin (H) gene places the respiroviruses basal to the avula-rubulavirus group, but the relationship of this lineage with henipa and morbillviruses is not resolved. Different genes may be under varying evolutionary pressures giving rise to these conflicting signals. Given the level of conservation in the M and L genes, we suggest that together with F gene, these or concatenated datasets for all six genes are likely to reveal the most reliable phylogenies at a family level, and should be used for future phylogenetic studies in this group. Split decomposition analysis suggests that recombination within genera, may have a contributed to the emergence of dolphin morbillivirus, and several species within respiroviruses. A partial L gene alignment, resolves the relationship of 25 unclassified paramxyoviruses into 4 clades (Chiopteran-, Salmon-, Rodentian- and Ophidian paramyxoviruses) which group with rubula-, respiro-, morbilliviruses, and within the paramxyovirinae respectively.

Newcastle disease: evolution of genotypes and the related diagnostic challenges

Since the discovery of Newcastle disease virus (NDV) in 1926, nine genotypes of class I viruses and ten of class II have been identified, representing a diverse and continually evolving group of viruses. The emergence of new virulent genotypes from global epizootics and the year-to-year changes observed in the genomic sequence of NDV of low and high virulence implies that distinct genotypes of NDV are simultaneously evolving at different geographic locations across the globe. This vast genomic diversity may be favored by the large variety of avian species susceptible to NDV infection and by the availability of highly mobile wild bird reservoirs. The genomic diversity of NDV increases the possibility of diagnostic failures, resulting in unidentified infections. Constant epidemiological surveillance and pro-active characterization of circulating strains are needed to ensure that the immunological and PCR reagents are effective in identifying NDV circulating worldwide. For example, in the United States, the widely used real-time reverse transcription polymerase chain reaction (RRT-PCR) matrix gene assay for the identification of NDV often fails to detect low virulence APMV-1 from waterfowl, while the RRT-PCR fusion gene assay, used to identify virulent isolates, often fails to detect certain virulent NDV genotypes. A new matrix-polymerase multiplex test that detects most of the viruses currently circulating worldwide and a modified fusion test for the identification of virulent pigeon viruses circulating in the U.S. and Europe have recently been developed. For newly isolated viruses with unknown sequences, recently developed random priming sequencing methods need to be incorporated into the diagnostic arsenal. In addition, the current system of classifying NDV into genotypes or lineages is inadequate. Here, we review the molecular epidemiology and recent diagnostic problems related to viral evolution of NDV and explain why a new system, based on objective criteria, is needed to categorize genotypes.

Comparison of paramyxovirus isolates from snakes, lizards and a tortoise

Previously uncharacterized paramyxovirus (PMV) isolates from four snakes, three lizards and a tortoise were compared based on partial sequences of the L, HN, and U genes. Analysis of the sequences supported the classification of all reptilian PMVs in a separate genus (Ferlavirus) in the subfamily Paramyxovirinae. Within each of the gene segments, the squamatid isolates could be divided into two groups with a sequence divergence of 0.3-15.6% nt (0-6.8% aa) within the groups and 19.5-22.3% nt (5-7.4% aa) between the groups for the L gene, and 0.9-15.4% nt (0-6.9% aa) within the groups and 18.2-22.5% nt (4.4-9.5% aa) between the groups for the HN gene while higher values of 0.4-17.1% nt (0-13.3% aa) within the groups and 28.9-31.3% nt (25.5-27.8% aa) between the groups were found for the U gene. Isolates from lizards were found in both groups. There was no host species specificity in the grouping of the isolates from snakes and lizards. However, the L gene sequence obtained from the tortoise isolate differed significantly from the sequences obtained from the snake and lizard isolates. This isolate showed divergence values of 24.2-27% nt (18.5-20.9% aa) compared to the squamatid sequences. The tortoise isolate clustered together with the other reptilian PMVs, but not into any of the squamatid groups on the phylogenetic tree. It is hypothesized that this chelonian PMV has a more unique genome sequence as neither HN nor U gene parts could be amplified using newly designed consensus nested PCRs.

Paramyxoviruses infecting humans: the old, the new and the unknown

Prior to the emergence of Hendra virus in Australia in 1994, paramyxoviruses were considered to be a taxonomic group of ubiquitous pathogens, consisting primarily of Biosafety Level 2 agents, which possessed narrow host ranges and often caused only mild or preventable diseases in humans and animals. In recent years, a number of Paramyxoviridae members have emerged, including previously unrecognized human pathogens and highly pathogenic zoonoses. The recent emergence of paramyxoviruses in humans suggests that there is an increased incidence of zoonotic transmission between wildlife, livestock and human hosts. This article explores the current body of scientific knowledge, disease burden and knowledge of reservoirs of these emerging paramyxoviruses and provides a comparative review of both older and emerging viruses that have been shown to infect humans.

Detection of a Broad Range of Class I and II Newcastle Disease Viruses Using a Multiplex Real-Time Reverse Transcription Polymerase Chain Reaction Assay

Prompt detection of virulent strains of Newcastle disease virus (vNDV) using real-time reverse transcription polymerase chain reaction (RT-PCR) is challenging because of the broad genetic variability across 2 clades comprising 18 recognized genotypes. A large proportion of class I low virulence ND viruses recently identified in samples recovered from wild birds and from poultry in live bird markets are not detected by the validated real-time RT-PCR assay that targets the matrix gene (M-gene assay). This study describes the identification and sequencing of a conserved region from the polymerase gene of class I NDV and the design and evaluation of a real-time RT-PCR assay (L-TET assay) that identifies a broad range of NDV, demonstrates a 10-fold increase in sensitivity over a previously reported L-gene assay, and works in conjunction with the existing M-gene assay using the same protocol. The L-TET assay detects ≤1 fg of homologous transcribed RNA from genotypes 5, 7, and 8 of class I, and from class II genotype II in either single- or multiplex format. Differential detection of mixed class I and II viruses down to 100 fg is possible because L-TET uses an alternate fluorophore from the M-gene assay. The multiplexed assay is capable of detecting a broad range of class I and II ND viruses with <1 threshold cycle decrease in sensitivity compared to the single probe. A total of 140 class I ( n = 108, genotypes 1–2 and 4–9) and class II ( n = 32, genotypes I–VII) were correctly identified by both the single- and multiplex formats.

Genomic comparison of the complete coding and intergenic regions of the VG/GA Newcastle disease virus and its respirotropic clone 5

The complete genome of the Villegas-Glisson/University of Georgia (VG/GA) strain of Newcastle disease virus (NDV) and that of a plaque purified clone (clone 5) exhibiting a respiratory phenotype were sequenced and analyzed. The VG/GA strain, isolated from the intestine of healthy turkeys, replicates in the respiratory and intestinal tract of chickens. It is used worldwide as a vaccine strain and its tissue tropism is extremely important for protection against velogenic viscerotropic NDV which targets both intestinal and respiratory epithelia, inducing severe gross and microscopic damage. The clone 5, a plaque purified clone from the VG/GA strain, cannot be recovered from the intestine of infected birds, suggesting a respirotropic nature. A modified primer sequence-independent amplification method was used to sequence the complete coding regions of both viruses and to assess phylogenetic relationships and genomic basis for phenotype differences. The phylogenetic analysis grouped the VG/GA strain and the clone 5 within class II, genotype II viruses and showed that they are greater than 99.9% identical with only 5 nucleotides differences. Both are closely related to classic vaccine strains, such as LaSota and B1. Only 3 amino acid differences at the fusion protein differentiated the VG/GA strain from the clone 5. These differences may explain the differential phenotype observed in the VG/GA strain and are discussed.

The large polymerase protein is associated with the virulence of Newcastle disease virus

Naturally occurring Newcastle disease virus (NDV) strains vary greatly in virulence, ranging from no apparent infection to severe disease causing 100% mortality in chickens. The viral determinants of NDV virulence are not completely understood. Cleavage of the fusion protein is required for the initiation of infection, and it acts as a determinant of virulence. The attachment protein HN was found to play a minor role in virulence. In this study, we have evaluated the role of the internal proteins (N, P, and L) in NDV virulence by using a chimeric reverse-genetics approach. The N, P, and L genes were exchanged individually between an avirulent NDV strain, LaSota, and an intermediate virulent NDV strain, Beaudette C (BC), and the N and P genes were also exchanged together. The recovered chimeric viruses were evaluated for their pathogenicity in the natural host, chickens. Our results showed that the pathogenicities of N and P chimeric viruses were similar to those of their respective parental viruses, indicating that the N and P genes probably play minor roles in virulence. However, replacement of the L gene of BC with that of LaSota significantly increased the pathogenicity of the L-chimeric virus, suggesting that the L gene probably contributes to the virulence of NDV. The L-chimeric BC virus was found to replicate at a 100-fold-higher level than its parental virus in chicken brain, suggesting that the increase in pathogenicity may be due to the increased replication level of the chimeric virus. Our findings offer new insights into the pathogenesis of NDV infection.

Pathotypical characterization and molecular epidemiology of Newcastle disease virus isolates from different hosts in China from 1996 to 2005

Thirty Newcastle disease virus (NDV) strains isolated from outbreaks in China during 1996 to 2005 were characterized pathotypically and genotypically. All strains except one were velogenic. An analysis of the variable region (nucleotides 47 to 420) of the F gene indicated that 6 isolates belonged to genotype II, 3 to genotype III, 1 (isolated from a pigeon) to genotype VI, and 20 to genotype VII. Isolates belonging to genotype VII were further divided into five subtypes, VIIa, VIIb, VIIc, VIId, and VIIe, and subtype VIId was made up of VIId1 to VIId5. These results showed that genotype VII isolates might have been the most prevalent in China during the past two decades. Genotype VII isolates shared high homology, but the homology was less than that between genotype VII viruses and the vaccine virus LaSota. Among these NDV isolates, 25 isolates had the velogenic motif (112)R/K-R-Q-K/R-R-F(117) that is consistent with results of the biological tests. However, four of five LaSota-type isolates that contained the lentogenic motif (112)G-R-Q-G-R-L(117) were velogenic, except SY/03, in the view of the biological test. The majority of genotype VII isolates had lost one or two N-glycosylation sites. Finally, a cross-protection experiment in which specific-pathogen-free chickens vaccinated with LaSota were challenged by six NDV isolates showed that more than three isolates were antigenic variants that could be responsible for recent outbreaks of Newcastle disease.

Identification of a natural multi-recombinant of Newcastle disease virus

Newcastle disease (ND), caused by ND virus (NDV), is one of the most serious illnesses of birds, particularly chickens, and has been one of the major causes of economic losses in the poultry industry. Live vaccines are widely used to prevent chicken from NDV all over the world. Given the implications that recombination has for RNA virus evolution, it is clearly important to determine the extent to which recombination plays a role in NDV evolution. In this study, we performed the phylogenetic and recombination analysis on complete NDV genomes. A natural multi-recombinant cockatoo/Indonesia/14698/90 (AY562985) was identified. Its two minor parental-like strains might be from the NDV vaccine lineage and anhinga/U.S.(Fl)/44083/93 lineage, respectively. Our study suggests that recombination plays a role in NDV evolution. Especially, the study also suggests that live vaccines have capacity to play roles in shaping NDV evolution by homologous recombination with circulating virus.

Characterization of a parainfluenza virus isolated from a bottlenose dolphin (Tursiops truncatus)

A novel member of the parainfluenza virus family was identified in a bottlenose dolphin with respiratory disease. The case animal was a 19-year old male Atlantic bottlenose dolphin (Tursiops truncatus) that presented with signs of respiratory illness, including raspy, foul-odored breaths and cream-colored exudate from the blowhole. Focally extensive pyogranulomatous bronchointerstitial pneumonia with moderate numbers of intralesional yeast organisms was identified on histopathological examination. Other significant microscopic findings included multifocal erosive and ulcerative tracheitis and laryngitis consisting of active laryngeal lymphatic tissue and dilated glands with eosinophilic fluid. The cause of death was attributed to respiratory disease of unknown etiology. In addition to the postmortem isolation of Candida glabrata and mixed bacteria from lung tissue, a virus was isolated from two antemortem affected lung aspirates collected over a 2-month period and two postmortem samples (mediastinal lymph node and left lung tissue homogenate). The morphology of the virions on negative staining and transmission electron microscopy was consistent with that of paramyxoviruses. Two genomic fragments, comprising 532 and 419 nucleotides from the open reading frames that code for the viral polymerase and fusion protein, respectively, were amplified by polymerase chain reaction using degenerate primers. Phylogenetic analyses of the two viral RNA segments showed that the isolate comprised a novel virus strain, tentatively named T. truncatus parainfluenza virus type 1 (TtPIV-1). The virus is monophyletic with, but genetically distinct from, the various bovine parainfluenza virus type 3 strains.

Isolation of avian paramyxovirus 1 from a patient with a lethal case of pneumonia

An unknown virus was isolated from a lung biopsy sample and multiple other samples from a patient who developed a lethal case of pneumonia following a peripheral blood stem cell transplant. A random PCR-based molecular screening method was used to identify the infectious agent as avian paramyxovirus 1 (APMV-1; a group encompassing Newcastle disease virus), which is a highly contagious poultry pathogen that has only rarely been found in human infections. Immunohistochemical analysis confirmed the presence of APMV-1 antigen in sloughed alveolar cells in lung tissue from autopsy. Sequence from the human isolate showed that it was most closely related to virulent pigeon strains of APMV-1. This is the most completely documented case of a systemic human infection caused by APMV-1 and is the first report of an association between this virus and a fatal disease in a human.

Genetic characterization of avian metapneumovirus subtype C isolated from pheasants in a live bird market

Complete nucleotide sequences of two avian metapneumoviruses (aMPV), designated PL-1 and PL-2, were isolated from pheasants, revealing novel sequences of the first aMPV to be fully sequenced in Korea. The complete genome of both PL-1 and PL-2 was composed of 13,170 nucleotides. Phylogenetic analysis revealed that PL-1 belonged to aMPV subtype C, sharing higher homology in deduced amino acid sequence identities with hMPV, rather than with aMPV subtypes A and B. Replication of PL-1 in experimentally re-infected pheasants was confirmed by reverse transcription (RT)-polymerase chain reaction (PCR). Chickens and mice were experimentally inoculated with PL-1 to test the replication potential of PL-1 in other species. Although one specimen from the nasal turbinates of an inoculated chicken showed a slight trace of viral replication at 3 days post-infection (dpi), all of the infected mice were negative for aMPV by RT-PCR throughout the experiment, suggesting that PL-1 does not readily infect mammals. This is the first report of the isolation and complete genomic sequence of aMPV subtype C originating from pheasants.

Third genome size category of avian paramyxovirus serotype 1 (Newcastle disease virus) and evolutionary implications

The goal of the study was to establish if there was a relationship between molecular patterns and virus evolution. Therefore the complete genome sequence of two distinct apathogenic Newcastle disease virus (NDV) strains was determined and a third genome size category, containing 15,198 nucleotides, was recognized. Phylogenetic analysis revealed that two major separations resulting in three genome size categories occurred during the history of NDV. An ancient division in the primordial reservoir (wild waterbird species) led to two basal sister clades, class I and II, with genome sizes 15,198 (due to a 12 nucleotide insert in the phosphoprotein gene) and 15,186 nucleotides, respectively. Ancestors of only class II viruses colonized chicken populations and subsequently converted to virulent forms. These took place more than once and resulted in an early lineage [including genotypes I-IV and H33(W)] with genome size of 15,186 nucleotides. A second division occurred in the 20th century in the secondary (chicken) host. This gave rise to the branching-off of a clade (including recent genotypes V-VIII consisting of only pathogenic viruses) with the concomitant insertion of six nucleotides into the 5' non-coding region of the nucleoprotein gene thereby increasing the genome size to 15,192 nucleotides.

Pathogenesis of Newcastle disease in commercial and specific pathogen-free turkeys experimentally infected with isolates of different virulence

The pathogenesis of five different Newcastle disease virus (NDV) isolates representing all pathotypes was examined in commercial and specific pathogen-free (SPF) turkeys. Experimentally-infected birds were monitored clinically and euthanatized, with subsequent tissue collection, for examination by histopathology, by immunohistochemistry for the presence of NDV nucleoprotein, and by in situ hybridization for the presence of replicating virus. Clinically, the lentogenic pathotype did not cause overt clinical signs in either commercial or SPF turkeys. Mesogenic viruses caused depression in some birds. Turkeys infected with velogenic neurotropic and velogenic viscerotropic isolates showed severe depression, and neurologic signs. Histologic appearances for all strains had many similarities to lesions observed in chickens inoculated with the various isolates; that is, lesions were present predominantly in lymphoid, intestinal, and central nervous tissues. However, in general, disease among turkeys was less severe than in chickens, and turkeys could be considered a subclinical carrier for some of the isolates.

Identification and subgrouping of pigeon type Newcastle disease virus strains by restriction enzyme cleavage site analysis

A host variant of Newcastle disease virus (NDV, genus Avulavirus, family Paramyxoviridae) is responsible for an autonomous disease in pigeons. It emerged in the late 1970s in the Mediterranean region. Despite great genetic diversity the vast majority of strains belong to a monophyletic group (sublineage VIb) within genotype VI of NDV strains that were indigenous in the region at that time. To date only a monoclonal antibody assay is available for the specific identification of pigeon type strains. A specific genetic assay is described suitable for the identification of pigeon isolates. Cleavage site analysis of a 1349 bp amplicon of the fusion protein gene was carried out using restriction enzymes (RE) HinfI, BstOI and RsaI. RE analysis of over 100 strains isolated between 1978 and 2002 deriving from 16 countries has revealed nine RE-patterns, which were progressive site variants of the parental (group VI) genotype. In spite of substantial site variation, extant pigeon viruses lacked a BstOI cleavage site at nucleotide 1601 shared by other NDV strains of chicken origin. RE analysis is a simple and reliable method both for the identification and subgrouping of pigeon type viruses.

Molecular Characterization of Virulent Newcastle Disease Virus Isolates from Chickens during the 1998 NDV Outbreak in Kazakhstan

Newcastle disease virus (NDV) infects domesticated and wild birds throughout the world and has the possibility to cause outbreaks in chicken flocks in future. To assess the evolutionary characteristics of 10 NDV strains isolated from chickens in Kazakhstan during 1998 we investigated the phylogenetic relationships among these viruses and viruses described previously. For genotyping, fusion (F) gene phylogenetic analysis (nucleotide number 47-421) was performed using sequences of Kazakhstanian isolates as compared to sequences of selected NDV strains from GenBank. Phylogenetic analysis showed that all newly characterized strains belonged to the genetic group designated as VIIb. All strains possessed a virulent fusion cleavage site (RRQRR/F) belonging to velogenic or mesogenic pathotypes with intracerebral pathogenicity indexes (ICPI) varying from 1.05 to 1.87.

Comparison of the full-length genome sequence of avian metapneumovirus subtype C with other paramyxoviruses

We determined the nucleotide (nt) sequence of the small hydrophobic (SH), attachment glycoprotein (G), and RNA polymerase (L) genes, plus the leader and trailer regions of the Colorado strain of Avian metapneumovirus subtype C (aMPV/C) in order to complete the genome sequencing. The complete genome comprised of 13,134 nucleotides, with a 40 nt leader at its 3' end and a 45 nt trailer at its 5' end. The aMPV/C L gene was the largest with 6173 nt and consisting of a single open reading frame encoding a 2005 amino acids (aa) protein. Comparison of the aMPV/C SH, G, and L nt and predicted aa sequences with those of Human metapneumoviruses (hMPV) revealed higher nt and aa sequence identities than the sequence identities between the aMPV subtypes A, B, C, and D, supporting earlier finding that aMPV/C was closer evolutionary to hMPV than the other aMPV subtypes.