Genomic characterization of a wild-bird-origin pigeon paramyxovirus type 1 (PPMV-1) first isolated in the northwest region of China

Molecular characteristics and phylogenetic analysis of pigeon paramyxovirus type 1 isolates from pigeon meat farms in Shanghai (2009-2012)

The majority of pigeon paramyxovirus type 1 (PPMV-1) strains are generally non-pathogenic to chickens; however, they can induce severe illness and high mortality rates in pigeons, leading to substantial economic repercussions. The genomes of 11 PPMV-1 isolates from deceased pigeons on meat pigeon farms during passive monitoring from 2009 to 2012 were sequenced and analyzed using polymerase chain reaction and phylogenetic analysis. The complete genome lengths of 11 isolates were approximately 15,192 nucleotides, displaying a consistent gene order of 3'-NP-P-M-F-HN-L-5'. ALL isolates exhibited the characteristic motif of 112RRQKRF117 at the fusion protein cleavage site, which is characteristic of velogenic Newcastle disease virus. Moreover, multiple mutations have been identified within the functional domains of the F and HN proteins, encompassing the fusion peptide, heptad repeat region, transmembrane domains, and neutralizing epitopes. Phylogenetic analysis based on sequences of the F gene unveiled that all isolates clustered within genotype VI in class II. Further classification identified at least two distinct sub-genotypes, with seven isolates classified as sub-genotype VI.2.1.1.2.2, whereas the others were classified as sub-genotype VI.2.1.1.2.1. This study suggests that both sub-genotypes were implicated in severe disease manifestation among meat pigeons, with sub-genotype VI.2.1.1.2.2 displaying an increasing prevalence among Shanghai's meat pigeon population since 2011. These results emphasize the value of developing pigeon-specific vaccines and molecular diagnostic tools for monitoring and proactively managing potential PPMV-1 outbreaks.

Comparative pathogenicity of a genotype XXI.1.2 pigeon Newcastle disease virus isolate in pigeons and chickens

Here, we performed molecular and pathogenic characterization of a Newcastle disease virus (NDV) isolate from pigeons in Bangladesh. Molecular phylogenetic analysis based on the complete fusion gene sequences classified the three study isolates into genotype XXI (sub-genotype XXI.1.2) together with recent NDV isolates obtained from pigeons in Pakistan (2014-2018). The Bayesian Markov Chain Monte Carlo analysis revealed that the ancestor of Bangladeshi pigeon NDVs and the viruses from sub-genotype XXI.1.2 existed in the late 1990s. Pathogenicity testing using mean embryo death time pathotyped the viruses as mesogenic, while all isolates carried multiple basic amino acid residues at the fusion protein cleavage site. Experimental infection of chickens and pigeons revealed no or minimum clinical signs in chickens, while a relatively high morbidity (70%) and mortality (60%) were observed in pigeons. The infected pigeons showed extensive and systemic lesions including hemorrhagic and/or vascular changes in the conjunctiva, respiratory and digestive system and brain, and atrophy in the spleen, while only mild congestion in the lungs was noticed in the inoculated chickens. Histologically, consolidation in the lungs with collapsed alveoli and edema around the blood vessels, hemorrhages in the trachea, severe hemorrhages and congestion, focal aggregation of mononuclear cells, and single hepatocellular necrosis in the liver, severe congestion, multifocal tubular degeneration, and necrosis, as well as mononuclear cell infiltration in the renal parenchyma, encephalomalacia with severe neuronal necrosis with neuronophagia were noticed in the brain in infected pigeons. In contrast, only slight congestion was found in lungs of the infected chickens. qRT-PCR revealed the replication of the virus in both pigeons and chickens; however, higher viral RNA loads were observed in oropharyngeal and cloacal swabs, respiratory tissues, and spleen of infected pigeons than the chickens. In conclusion, genotype XXI.1.2 NDVs are circulating in the pigeon population of Bangladesh since 1990s, produce high mortality in pigeons with pneumonia, hepatocellular necrosis, renal tubular degeneration, and neuronal necrosis in pigeons, and may infect chickens without overt signs of clinical disease and are likely to shed viruses via the oral or cloacal routes.

A pigeon paramyxovirus type 1 isolated from racing pigeon as an inactivated vaccine candidate provides effective protection

Pigeon paramyxovirus type 1 (PPMV-1), a variant of Newcastle disease virus (NDV), causes severe Newcastle disease (ND) in pigeons. However, there is no PPMV-1 vaccine available worldwide. In this study, a strain of PPMV-1 was isolated from outbreaks in a vaccinated racing pigeon (Columbia livia) loft in China, namely, PPMV-1/pigeon/Gansu/China/02/2020 (GS02). Experimental infection with GS02 showed mortality rates of 100% and 87.50% in 4- and 12-week-old pigeons, respectively, suggesting that GS02 is virulent and more sensitive to young pigeons. The whole genome of GS02 determined the fusion (F) protein possessing virulence cleavage site ¹¹²RRQKRF¹¹⁷. Phylogenetic analysis indicated that GS02 was a subgenotype VI.2.1.1.2.2 (VIk) of Class II NDV and more closely related to the JS/06/20/Pi (MW271791) strain, but it was far from the genetic distance from the commercial vaccine chicken-origin La Sota strain. Using inactivated GS02 as a vaccine candidate and inactivated vaccine La Sota to immunize the pigeons, both of them provided complete protection against GS02 challenge. The GS02 vaccine candidate induced higher antibody titers than the La Sota vaccine, and cross-reactivity testing showed antigenically slight differences between GS02 and La Sota. These results indicated that the GS02 candidate could be a potential pigeon-derived vaccine for the prevention and control of PPMV-1 in pigeons.

A molecular, epidemiological and pathogenicity analysis of pigeon paramyxovirus type 1 viruses isolated from live bird markets in China in 2014-2021

To expand our understanding of the epidemiology of pigeon paramyxovirus type 1 (PPMV-1) in China, risk-based active surveillance was undertaken with pigeon swabs collected from live bird markets in 2014-2021. Seventy-six PPMV-1 strains were isolated from 12 provinces (60%) of the 20 provinces surveyed, and the positive rates of PPMV-1 varied from 0.50% to 3.19% annually. The complete genomic sequences of 18 representative viruses were analyzed, revealing a genome of 15,192 nucleotides, with the gene order 3'-NP-P-M-F-HN-L-5'. All isolates contained the ¹¹²RRQKRF¹¹⁷ cleavage site in the fusion (F) protein, a characteristic generally associated with virulent Newcastle disease viruses (NDVs), and the intracerebral pathogenicity index values (1.05-1.41) of four isolates indicated their virulence. A challenge experiment also demonstrated that all four isolates are pathogenic to pigeons, with morbidity rates of 60-100% and mortality rates of 0-30%. A further analysis of the functional domains of the F and HN proteins revealed several mutations in the fusion peptide, signal peptide, neutralizing epitopes, heptad repeat region, and transmembrane domains, and the substitution of cysteine residue 25 (C25Y) and substitutions in the HRb region (V287I) of the F protein and the transmembrane domain (V45A) of the HN protein may play important roles in PPMV-1 virulence. In a phylogenetic analysis based on the complete sequences of the F gene, all eighteen isolates all clustered into sub-genotype VI.2.1.1.2.2 (VIb) in class II, and shared high nucleotide sequence identity, indicating that the PPMV-1 strains in sub-genotype VI.2.1.1.2.2 are the predominant PPMV-1 viruses in pigeons in China and that the variations in these viruses have been relatively stable over the past 8 years. This study identifies the genetic and pathogenicity characteristics of the PPMV-1 strains prevalent in China and extends our understanding of the prevalence of this virus in China.

A Pigeon-Derived Sub-Genotype XXI.1.2 Newcastle Disease Virus from Bangladesh Induces High Mortality in Chickens

Newcastle disease virus (NDV) is a significant pathogen of poultry; however, variants also affect other species, including pigeons. While NDV is endemic in Bangladesh, and poultry isolates have been recently characterized, information about viruses infecting pigeons is limited. Worldwide, pigeon-derived isolates are commonly of low to moderate virulence for chickens. Here, we studied a pigeon-derived NDV isolated in Bangladesh in 2010. To molecularly characterize the isolate, we sequenced its complete fusion gene and performed a comprehensive phylogenetic analysis. We further studied the biological properties of the virus by estimating mean death time (MDT) and by experimentally infecting 5-week-old naïve Sonali chickens. The studied virus clustered in sub-genotype XXI.1.2 with NDV from pigeons from Pakistan isolated during 2014–2018. Deduced amino acid sequence analysis showed a polybasic fusion protein cleavage site motif, typical for virulent NDV. The performed in vivo pathogenicity testing showed a MDT of 40.8 h, and along with previously established intracerebral pathogenicity index of 1.51, these indicated a velogenic pathotype for chickens, which is not typical for pigeon-derived viruses. The experimental infection of chickens resulted in marked neurological signs and high mortality starting at 7 days post infection (dpi). Mild congestion in the thymus and necrosis in the spleen were observed at an advanced stage of infection. Microscopically, lymphoid depletion in the thymus, spleen, and bursa of Fabricius were found at 5 dpi, which progressed to severe in the following days. Mild to moderate proliferation of glial cells was noticed in the brain starting at 2 dpi, which gradually progressed with time, leading to focal nodular aggregation. This study reports the velogenic nature for domestic chickens of a pigeon-derived NDV isolate of sub-genotype XXI.1.2. Our findings show that not all pigeon-derived viruses are of low virulence for chickens and highlight the importance of biologically evaluating the pathogenicity of NDV isolated from pigeons.

Isolation and Pathogenic Characterization of Pigeon Paramyxovirus Type 1 via Different Inoculation Routes in Pigeons

Pigeon paramyxovirus type I (PPMV-1) causes regular outbreaks in pigeons and even poses a pandemic threat among chickens and other birds. The birds infected with PPMV-1 mainly show a pathological damage in the respiratory system, digestive system, and nervous system. However, there were few reports on the efficiency of the virus entering the host via routes of different systems. In the present study, a PPMV-1 strain was obtained from a dead wild pigeon in 2016 in Beijing, China. The mean death time (MDT) and the intracerebral pathogenicity (ICPI) of our isolate showed medium virulence. Phylogenetic analysis based on F gene sequence showed that the isolate belonged to subgenotype VIb, class II, which dominated in China in recent years. Then, we evaluated the infection efficiency of different routes. Pigeons were randomly divided into five groups of six as follows: intracephalic (IC), intranasal (IN), and intraoral (IO) infection routes, cohabitation infection (CO), and negative control (N negative). All pigeons were inoculated with 100 μl·10⁶ EID₅₀ PPMV-1 virus. After infection, pathological lesions, virus shedding, body weight change, survival rate, and tissue tropism were tested to compare the efficiency of the different infected routes. The mortality of groups IC, IN, IO, and CO were 100, 66.7, 50, and 33.3%, respectively. Weight loss in group IC was higher than the other groups, followed by groups IN and IO. The lesions observed in PPMV-1-infected pigeons were severe, especially in the lung and intestine in group IC. Viral shedding was observed from 2 dpi in groups IC and IN, but the shedding rate was higher in group IN than group IC. The longest period was in group CO. Tissue tropism experiment showed that our isolate has a wide range of tissue distribution, and the virus titer in the heart and intestine of group IC and in the brain of group IN was higher. Our data may help us to evaluate the risk of transmission of PPMV-1.

Comparative biology of two genetically closely related Newcastle disease virus strains with strongly contrasting pathogenicity

A lentogenic strain of Newcastle disease virus (NDV) with an intracerebral pathogenicity index (ICPI) of 0.36 was derived by the passage of a mesogenic NDV isolate with an original ICPI of 1.04. Animal experiments showed that the original strain caused much severer clinical signs and mortality than the derived strain in chickens. To elucidate the molecular reason for this virulence change, the complete viral genomes of the original and derived strains were sequenced. Molecular analysis showed that both viruses contained the same fusion (F) protein with a cleavage site (Fcs) motif that is usually associated with velogenic viruses. Molecular comparison revealed five amino acid (aa) differences in nucleoprotein (NP) (aa 426), hemagglutinin-neuraminidase (HN) (aas 215 and 430), and large protein (L) (aas 1694 and 1767), accompanied by the changes of relevant biological activities in membrane fusion and replication. Thus, we believe that the virulence changes may induced by these mutations. Our findings make a foundation for more in-depth investigations of the molecular mechanism underlying virulence.

Innate immune responses of domestic pigeons to the infection of pigeon paramyxovirus type 1 virus

Pigeon paramyxovirus type 1 (PPMV-1) is a globally distributed, virulent member of the avian paramyxovirus type-1. The PPMV-1-associated disease poses a great threat to the pigeon industry. The innate immune response is crucial for antiviral infections and revealing the pathogenic mechanisms of PPMV-1. In this study, we evaluated the pathogenicity of a PPMV-1 strain LHLJ/110822 in one-month-old domestic pigeons, as well as the host immune responses in PPMV-1-infected pigeons. We observed typically clinical sign in infected pigeons by 3 dpi. The morbidity rate and the mortality in pigeons inoculated with the PPMV-1 strain were up to 100% and 30%, respectively. The virus could replicate in all of the examined tissues, namely trachea, lung, liver, spleen, and bursa of Fabricius. In addition, the infected pigeons had developed anti-PPMV-1 antibodies as early as 8 dpi; and the antibody level increased over the time in this study. The expression level of toll-like receptor (TLR) 2, TLR3 TLR15, IFN-γ, and IL-6 were significantly upregulated by the PPMV-1 infection in some tissues of pigeons. By contrast, PPMV-1 infection results in downregulation of IL-18 expression in most of investigated tissues except for bursa of Fabricius in this study. The current results confirmed that this virus could replicate in pigeons and induce host immune responses, then leading to produce serum antibody titers. Meanwhile, the PPMV-1 infection induces strong innate immune responses and intense inflammatory responses at early stage in pigeon which may associate with the viral pathogenesis.

Comparative pathogenicity of two closely related Newcastle disease virus isolates from chicken and pigeon respectively

Newcastle disease (ND), caused by virulent Newcastle disease virus (NDV), is a highly contagious disease that has led to tremendous economic losses worldwide. Pigeon paramyxovirus type 1 (PPMV-1) is an antigenic and host variant of NDV. However, limited in-depth studies are available concerning side-by-side comparison of pathogenicity of PPMV-1 and its phylogenetically close NDV both in chickens and pigeons. To this end, two phylogenetically closely related NDV isolates, Kuwait 256 and JS/07/04/Pi from chicken and pigeon respectively were pathotypically and genotypically characterized in this study. The results indicated that Kuwait 256 was a velogenic strain, while JS/07/04/Pi was a mesogenic strain based on the mean death time of chick embryos (MDT) and intracerebral pathogenicity index in 1-day-old chicks (ICPI). Pathogenicity tests showed that Kuwait 256 caused severe clinical signs and 100 % mortality, while JS/07/04/Pi caused no apparent disease in chickens. Interestingly, both Kuwait 256 and JS/07/04/Pi caused morbidity and mortality in pigeons. Notably, pigeons infected with JS/07/04/Pi exhibited viral shedding for longer time compared to Kuwait 256-infected pigeons. Collectively, the findings of this study suggested that PPMV-1 decreased the pathogenicity in chickens but gained a survival advantage over NDV of chicken origin after its adaptive variation in pigeons based on the previous evidence that PPMV-1 originated from chicken-origin viruses. This study laid the foundation for the elucidation of the molecularmechanism underlying difference in pathogenicity of PPMV-1 and chicken-origin NDV in chickens.

NP protein and F protein of pigeon paramyxovirus type 1 are associated with its low pathogenicity in chickens

In this study, we investigated which structural proteins of pigeon paramyxovirus type 1 (PPMV-1) are responsible for its low pathogenicity in chickens. The results revealed that the pathogenicity of the virus is determined by multiple genes. The NP protein and F protein were found to have the strongest individual effect on virulence, and this effect further enhanced when the two proteins were expressed in combination. Our study highlights the influence of the NP and F proteins on the pathogenicity of PPMV-1 in chickens.

Molecular characterization of two novel sub-sublineages of pigeon paramyxovirus type 1 in China

Pigeon paramyxovirus type 1 (PPMV-1) infection is enzootic in pigeon flocks and poses a potential risk to the poultry industry in China. To gain insight into the biological characteristics and transmission routes of circulating PPMV-1 in pigeons, 13 PPMV-1 isolates from domestic pigeons isolated during 2011-2015 in Guangxi province, China, were characterized using a pathogenicity assessment and phylogenetic analysis. All PPMV-1 isolates were mesogenic or lentogenic strains and had a mean death time (MDT) in 9-day-old SPF chicken embryos and a intracerebral pathogenicity index (ICPI) values of 54-154 h and 0.00-0.90, respectively. Analysis of the F and HN gene sequences of the PPMV-1 isolates and the Newcastle Disease (ND) vaccine strain La Sota, revealed that the nucleotide sequence similarity of the F and HN genes were all < 85% between the PPMV-1 isolates and La Sota, significantly lower than those > 98% among the PPMV-1 isolates. The amino acids sequence of the F protein at the cleavage site of the 13 PPMV-1 isolates was ¹¹²RRQKR↓F¹¹⁷, characteristic of virulent Newcastle disease virus (NDV). All 13 isolates were classified as sublineage 4b by phylogenetic analysis and evolutionary distances, based on the F gene sequences. It was also found that the 13 isolates were divided into two novel sub-groups of sublineage 4b, sub-sublineages 4biig and 4biih. Since these two novel sub-sublineages had two different geographic sources, we speculated that they represent two different transmission routes of PPMV-1 in China. Phylogenetic analysis of these isolates will help to elucidate the sources of the transmission and evolution of PPMV-1 and may help to control PPMV-1 infection in the pigeon industry in China.

Phylogenetic Analysis of Pigeon Paramyxoviruses Type-1 Identified in Mourning Collared-doves ( Streptopelia decipiens) in Namibia, Africa

We generated the complete sequence of the fusion ( F) protein gene from six pigeon paramyxoviruses type 1 (PPMV-1) isolated from Mourning Collared-doves ( Streptopelia decipiens) in Namibia, Africa between 2016 and 2017. All of the isolates had an F gene cleavage site motif of ¹¹²RRQKRF¹¹⁷ characteristic of virulent viruses. A phylogenetic analysis using the full F gene sequence revealed that the viruses belonged to genotype VIa and were epidemiologically related to PPMV-1s from Asia, Europe, and North America.

Phylogenetic and pathogenic characterization of a pigeon paramyxovirus type 1 isolate reveals cross-species transmission and potential outbreak risks in the northwest region of China

Pigeon paramyxovirus type-1 (PPMV-1) is enzootic in pigeons, causing severe economic loss in the poultry industry in many countries. However, the exact epidemic process of PPMV-1 transmission is still unclear. In this study, we analyzed the complete genome of the PPMV-1/SX-01/15 isolate. Sequence results show that the virus genome contains 15,192 nucleotides, with the gene order 3'-NP-P-M-F-HN-L-5'. Phylogenetic analysis revealed that this genome belongs to subgenotype VIc in class II. The mean death time (MDT) and intracerebral pathogenicity index (ICPI) were 62.4 h and 1.13, respectively, indicating that this isolate is a mesogenic PPMV-1 strain. To our knowledge, this is the first report of a subgenotype VIc mesogenic PPMV-1 strain circulating in commercial pigeon flocks in the northwest region of China. In a comparative infection experiment, the morbidity and mortality rates were 100% and 80%, respectively, in 4-week-old pigeons, whereas they were 50% and 30%, respectively, in 5-week-old chickens. Furthermore, this virus caused severe neurological symptoms in a 4-week-old pigeon and mild neurological symptoms in a 5-week-old chicken. A histopathological examination of the brain showed a classical nonsuppurative encephalitis lesion. The pattern of viral shedding, and viral load, and virus distribution differed between infected chickens and pigeons. Genomic characteristics suggest that there was cross-species transmission of PPMV-1 subgenotype VIc in this region at least from the years 2006 to 2015.