Successful establishment and global dispersal of genotype VI avian paramyxovirus serotype 1 after cross species transmission

Chong, Yee Ling; Lam, Tommy Tsan-Yuk; Kim, Oekyung; Lu, Huaguang; Dunn, Patricia A.; Poss, Mary

doi:10.1016/j.meegid.2013.04.025

Cited by 25 publications

(31 citation statements)

References 58 publications

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“…Indeed, the long period to the separation of class I and class II (approximately 234-244 years before the most recent isolates included in this study) and the small differences in CAI of these two classes provides evidence to suggest that the codon adaptation of APMV-1 is a slow process. As expected, class II genotype VI emerged from common ancestors with genotype VII (and genotypes XIII, XIV, XVII and XVIII) sometime between 1947 and 1951 (Table 2), that is in agreement with previously reported estimates (Chong et al, 2013;Sonora et al, 2015). Despite the differences in host of isolation for viruses of genotypes VI and VII, there are no large differences in codon usage or host adaptation, as it would be expected from a slow process of adaptation.…”

Section: Codon Usage Adaptation In Apmv-1 Is a Slow Processsupporting

confidence: 90%

Genome-wide analysis reveals class and gene specific codon usage adaptation in avian paramyxoviruses 1

Taylor

Dimitrov

Afonso

2017

Infection, Genetics and Evolution

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In order to characterize the evolutionary adaptations of avian paramyxovirus 1 (APMV-1) genomes, we have compared codon usage and codon adaptation indexes among groups of Newcastle disease viruses that differ in biological, ecological, and genetic characteristics. We have used available GenBank complete genome sequences, and compared codon usage of class I (CI-29 sequences containing 132,675 codons) and class II (CII-259 sequences containing 1,184,925 codons) APMV-1 genomes. We also compared available complete fusion protein gene sequences (CI-175 sequences containing 96,775 codons; CII-1166 sequences containing 644,798 codons). Adaptation to Gallus gallus was compared among the different classes of viruses, among different genomic regions based on transcriptional levels, or among the fusion gene. Interestingly, distinctive codon usage determined by differences in relative synonymous codon usage and by codon adaptation indexes was observed for the two APMV-1 classes and for different transcriptional regions within classes. Furthermore, differential use of the third codon position and preferential use of codon pairs were seen for the two different classes and for selected genotypes of class II despite the fact that there were no large differences in nucleotide composition. The data suggest that codon usage has changed significantly since the two APMV-1 classes diverged, however, these changes are not significantly pronounced among viruses of the same genotype, suggesting that codon adaptation in APMV-1 occurs through a slow evolutionary process.

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Section: Codon Usage Adaptation In Apmv-1 Is a Slow Processsupporting

confidence: 90%

Genome-wide analysis reveals class and gene specific codon usage adaptation in avian paramyxoviruses 1

Taylor

Dimitrov

Afonso

2017

Infection, Genetics and Evolution

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“…Poultry trade, however, does not explain all global movement of class II viruses. Rather, as demonstrated by our genotype VI-restricted model and a previously published genotype VI phylodynamic analysis [34], global migration of APMV-1 is also driven by transportation of pigeons, resulting in viral dispersal from Europe to other regions, including Africa and East Asia.…”

Section: Discussionmentioning

confidence: 63%

Global phylodynamic analysis of avian paramyxovirus-1 provides evidence of inter-host transmission and intercontinental spatial diffusion

et al. 2019

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Background: Avian avulavirus (commonly known as avian paramyxovirus-1 or APMV-1) can cause disease of varying severity in both domestic and wild birds. Understanding how viruses move among hosts and geography would be useful for informing prevention and control efforts. A Bayesian statistical framework was employed to estimate the evolutionary history of 1602 complete fusion gene APMV-1 sequences collected from 1970 to 2016 in order to infer viral transmission between avian host orders and diffusion among geographic regions. Ancestral states were estimated with a non-reversible continuous-time Markov chain model, allowing transition rates between discrete states to be calculated. The evolutionary analyses were stratified by APMV-1 classes I (n = 198) and II (n = 1404), and only those sequences collected between 2006 and 2016 were allowed to contribute host and location information to the viral migration networks. Results: While the current data was unable to assess impact of host domestication status on APMV-1 diffusion, these analyses supported the sharing of APMV-1 among divergent host taxa. The highest supported transition rate for both classes existed from domestic chickens to Anseriformes (class I:6.18 transitions/year, 95% highest posterior density (HPD) 0.31-20.02, Bayes factor (BF) = 367.2; class II:2.88 transitions/year, 95%HPD 1.9-4.06, BF = 34,582.9). Further, among class II viruses, domestic chickens also acted as a source for Columbiformes (BF = 34,582.9), other Galliformes (BF = 34,582.9), and Psittaciformes (BF = 34,582.9). Columbiformes was also a highly supported source to Anseriformes (BF = 322.0) and domestic chickens (BF = 402.6). Additionally, our results provide support for the diffusion of viruses among continents and regions, but no interhemispheric viral exchange between 2006 and 2016. Among class II viruses, the highest transition rates were estimated from South Asia to the Middle East (1.21 transitions/year; 95%HPD 0.36-2.45; BF = 67,107. 8), from Europe to East Asia (1.17 transitions/year; 95%HPD 0.12-2.61; BF = 436.2) and from Europe to Africa (1.06 transitions/year, 95%HPD 0.07-2.51; BF = 169.3). Conclusions: While migration appears to occur infrequently, geographic movement may be important in determining viral diversification and population structure. In contrast, inter-order transmission of APMV-1 may occur readily, but most events are transient with few lineages persisting in novel hosts.

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“…The deduction was further supported by the migration link from Europe to East China in the diffusion processes of VI.2.1.1.2.2 PPMV-1. Previous studies demonstrated that the European continent was the epicenter of global dissemination of PPMV-1 due to the movement of pigeons [39,40]. Cai et al [16] also proved that the VI viruses (P4 and W4) of China originated in Europe.…”

Section: Discussionmentioning

confidence: 99%

Evolutionary Dynamics and Age-Dependent Pathogenesis of Sub-Genotype VI.2.1.1.2.2 PPMV-1 in Pigeons

Xie

Chen

Zhang

et al. 2020

Viruses

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Pigeon paramyxovirus type 1 (PPMV-1) infection causes high morbidity in pigeons, resulting in a significant burden to the poultry industry. In this study, we isolated three PPMV-1 strains from diseased pigeons collected in Guangdong Province, South China, from June 2017 to April 2019. Genetic analysis revealed that these three PPMV-1 strains and most of the PPMV-1 strains isolated from China after 2011 were clustered into sub-genotype VI.2.1.1.2.2. Our Bayesian analysis revealed that the VI.2.1.1.2.2 viruses might have originated in Europe. Phylogeographic analyses revealed that East and South China might have played a key role in seeding the VI.2.1.1.2.2 PPMV-1 epidemic in China. To characterize the effect of age at infection on the outcome of PPMV-1 infection in pigeons, we investigated the pathogenesis and transmission of the pigeon/Guangdong/GZ08/2017 (GZ08) virus in 3-, 6-, and 12-week-old pigeons. Two of six 12-week-old pigeons inoculated with GZ08 survived, and all of the 3- and 6-week-pigeons inoculated with GZ08 died. Moreover, the GZ08 virus could be transmitted to 3-, 6-, and 12-week-old naïve contact pigeons. The lethality of the GZ08 virus through contact with 3-, 6-, and 12-week-old pigeons was 100%, 66.7%, and 0%, respectively, suggesting that the transmissibility of the GZ08 virus was stronger in young pigeons. These findings demonstrated that East and South China was the epicenter for dissemination of VI.2.1.1.2.2 PPMV-1, and age at infection has an impact on the outcome of PPMV-1 infection in pigeons.

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Successful establishment and global dispersal of genotype VI avian paramyxovirus serotype 1 after cross species transmission

Cited by 25 publications

References 58 publications

Genome-wide analysis reveals class and gene specific codon usage adaptation in avian paramyxoviruses 1

Genome-wide analysis reveals class and gene specific codon usage adaptation in avian paramyxoviruses 1

Global phylodynamic analysis of avian paramyxovirus-1 provides evidence of inter-host transmission and intercontinental spatial diffusion

Evolutionary Dynamics and Age-Dependent Pathogenesis of Sub-Genotype VI.2.1.1.2.2 PPMV-1 in Pigeons

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