Transmission dynamics of re-emerging rabies in domestic dogs of rural China

Tian, Huaiyu; Feng, Yue; Vrancken, Bram; Cazelles, Bernard; Tan, Hua; Gill, Mandev S.; Yang, Qiqi; Li, Yidan; Yang, Wei; Zhang, Yuzhen; Zhang, Yunzhi; Lemey, Philippe; Pybus, Oliver G.; Stenseth, Nils Chr.; Zhang, Hailin; Dellicour, Simon

doi:10.1371/journal.ppat.1007392

Cited by 39 publications

(54 citation statements)

References 56 publications

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“…These values are much higher than, for instance, estimates previously reported for rabies virus spread ( Dellicour et al. 2017 , 2019 ; Tian et al. 2018 ) but still lower than, for instance, the weighted branch dispersal velocity estimated for the West Nile virus spread in North America (255 km/year, 95% HPD [231, 286]) ( Pybus et al.…”

Section: Discussionmentioning

confidence: 59%

Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus

et al. 2020

Molecular Biology and Evolution

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107

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Abstract The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown once again that coronavirus (CoV) in animals are potential sources for epidemics in humans. Porcine deltacoronavirus (PDCoV) is an emerging enteropathogen of swine with a worldwide distribution. Here, we implemented and described an approach to analyze the epidemiology of PDCoV following its emergence in the pig population. We performed an integrated analysis of full genome sequence data from 21 newly sequenced viruses, along with comprehensive epidemiological surveillance data collected globally over the last 15 years. We found four distinct phylogenetic lineages of PDCoV, which differ in their geographic circulation patterns. Interestingly, we identified more frequent intra- and interlineage recombination and higher virus genetic diversity in the Chinese lineages compared with the USA lineage where pigs are raised in different farming systems and ecological environments. Most recombination breakpoints are located in the ORF1ab gene rather than in genes encoding structural proteins. We also identified five amino acids under positive selection in the spike protein suggesting a role for adaptive evolution. According to structural mapping, three positively selected sites are located in the N-terminal domain of the S1 subunit, which is the most likely involved in binding to a carbohydrate receptor, whereas the other two are located in or near the fusion peptide of the S2 subunit and thus might affect membrane fusion. Finally, our phylogeographic investigations highlighted notable South-North transmission as well as frequent long-distance dispersal events in China that could implicate human-mediated transmission. Our findings provide new insights into the evolution and dispersal of PDCoV that contribute to our understanding of the critical factors involved in CoVs emergence.

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Section: Discussionmentioning

confidence: 59%

Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus

et al. 2020

Molecular Biology and Evolution

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107

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“…Velocity may also be faster through higher elevations in the Front Range as puma are more likely to rapidly move through unsuitable habitat. Unsuitable habitat has also been demonstrated to increase the velocity of rabies lineages in dogs 49 . We acknowledge that in this study we did not sample all pumas in the system nor between the two sampled regions, and that FIV pco could not always be sequenced.…”

Section: Discussionmentioning

confidence: 99%

Host relatedness and landscape connectivity shape pathogen spread in the puma, a large secretive carnivore

et al. 2021

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Urban expansion can fundamentally alter wildlife movement and gene flow, but how urbanization alters pathogen spread is poorly understood. Here, we combine high resolution host and viral genomic data with landscape variables to examine the context of viral spread in puma (Puma concolor) from two contrasting regions: one bounded by the wildland urban interface (WUI) and one unbounded with minimal anthropogenic development (UB). We found landscape variables and host gene flow explained significant amounts of variation of feline immunodeficiency virus (FIV) spread in the WUI, but not in the unbounded region. The most important predictors of viral spread also differed; host spatial proximity, host relatedness, and mountain ranges played a role in FIV spread in the WUI, whereas roads might have facilitated viral spread in the unbounded region. Our research demonstrates how anthropogenic landscapes can alter pathogen spread, providing a more nuanced understanding of host-pathogen relationships to inform disease ecology in free-ranging species.

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Section: Discussionmentioning

confidence: 99%

Host relatedness and landscape connectivity shape pathogen spread in a large secretive carnivore

Fountain-Jones

Kraberger

Gagne

et al. 2019

Preprint

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Urban expansion can fundamentally alter wildlife movement and gene flow, but how urbanization alters pathogen spread is poorly understood. Here we combine high resolution host and viral genomic data with landscape variables to examine the context of viral spread in puma from two contrasting regions: one bounded by the wildland urban interface (WUI) and one unbounded with minimal anthropogenic development. We found landscape variables and host gene flow explained significant amounts of variation of feline immunodeficiency virus (FIV) spread in the WUI, but not in the unbounded region. The most important predictors of viral spread also differed; host spatial proximity, host relatedness, and mountain ranges played a role in FIV spread in the WUI, whereas unpaved roads were more important in the unbounded region. Our research demonstrates how anthropogenic landscapes can alter pathogen spread, providing a more nuanced understanding of host-pathogen relationships to inform disease ecology in free-ranging species.

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Transmission dynamics of re-emerging rabies in domestic dogs of rural China

Cited by 39 publications

References 56 publications

Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus

Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus

Host relatedness and landscape connectivity shape pathogen spread in the puma, a large secretive carnivore

Host relatedness and landscape connectivity shape pathogen spread in a large secretive carnivore

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