Spatio‐temporal analysis of Nova virus, a divergent hantavirus circulating in the European mole in Belgium

Laenen, Lies; Dellicour, Simon; Vergote, Valentijn; Nauwelaers, Inne; Coster, Sarah De; Verbeeck, Ina; Vanmechelen, Bert; Lemey, Philippe

doi:10.1111/mec.13887

Cited by 28 publications

(28 citation statements)

References 80 publications

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“…For this purpose, we used an analytical workflow already described in previous studies (e.g. Laenen et al 2016, Dellicour et al 2017 and implemented in the R package "seraphim" (Dellicour et al 2016a(Dellicour et al , 2016b. Here, we investigated the impact of the following environmental factors (Supplementary Figure S4): elevation, land cover variables ("croplands", "forests", "savannas"), inaccessibility (quantified as the time it takes to travel to the nearest major city of >50,000 inhabitants), as well as human, chicken and duck population densities.…”

Section: Resultsmentioning

confidence: 99%

Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference — Application to H5N1 spread in the Mekong region

et al. 2019

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Motivation The potentially low precision associated with the geographic origin of sampled sequences represents an important limitation for spatially explicit (i.e. continuous) phylogeographic inference of fast-evolving pathogens such as RNA viruses. A substantial proportion of publicly available sequences is geo-referenced at broad spatial scale such as the administrative unit of origin, rather than more precise locations (e.g. geographic coordinates). Most frequently, such sequences are either discarded prior to continuous phylogeographic inference or arbitrarily assigned to the geographic coordinates of the centroid of their administrative area of origin for lack of a better alternative. Results We here implement and describe a new approach that allows to incorporate heterogeneous prior sampling probabilities over a geographic area. External data, such as outbreak locations, are used to specify these prior sampling probabilities over a collection of sub-polygons. We apply this new method to the analysis of highly pathogenic avian influenza H5N1 clade data in the Mekong region. Our method allows to properly include, in continuous phylogeographic analyses, H5N1 sequences that are only associated with large administrative areas of origin and assign them with more accurate locations. Finally, we use continuous phylogeographic reconstructions to analyse the dispersal dynamics of different H5N1 clades and investigate the impact of environmental factors on lineage dispersal velocities. Availability and implementation Our new method allowing heterogeneous sampling priors for continuous phylogeographic inference is implemented in the open-source multi-platform software package BEAST 1.10. Supplementary information Supplementary data are available at Bioinformatics online.

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Section: Resultsmentioning

confidence: 99%

Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference — Application to H5N1 spread in the Mekong region

et al. 2019

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“…This discovery marks the second hantavirus, in addition to Nova virus ( Kang, Bennett, et al. 2011 ; Laenen et al. 2016 ), in the European mole.…”

Section: Introductionmentioning

confidence: 82%

A Novel Hantavirus of the European Mole, Bruges Virus, Is Involved in Frequent Nova Virus Coinfections

Laenen

Vergote

Kafetzopoulou

et al. 2017

Genome Biology and Evolution

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Hantaviruses are zoonotic viruses with a complex evolutionary history of virus–host coevolution and cross-species transmission. Although hantaviruses have a broad reservoir host range, virus–host relationships were previously thought to be strict, with a single virus species infecting a single host species. Here, we describe Bruges virus, a novel hantavirus harbored by the European mole (Talpa europaea), which is the well-known host of Nova virus. Phylogenetic analyses of all three genomic segments showed tree topology inconsistencies, suggesting that Bruges virus has emerged from cross-species transmission and ancient reassortment events. A high number of coinfections with Bruges and Nova viruses was detected, but no evidence was found for reassortment between these two hantaviruses. These findings highlight the complexity of hantavirus evolution and the importance of further investigation of hantavirus–reservoir relationships.

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“…Our analytical framework investigating the impact of environmental factors on lineage dispersal velocity comprised four distinct steps, which were previously applied in other studies (e.g., Dellicour, Rose, & Pybus, ; Laenen et al, ). The first step consisted in extracting the spatio‐temporal information embedded in a collection of posterior trees obtained using continuous phylogeographic inference.…”

Section: Methodsmentioning

confidence: 99%

Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages — Application to rabies virus spread in Iran

et al. 2019

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Recent years have seen the extensive use of phylogeographic approaches to unveil the dispersal history of virus epidemics. Spatially explicit reconstructions of viral spread represent valuable sources of lineage movement data that can be exploited to investigate the impact of underlying environmental layers on the dispersal of pathogens. Here, we performed phylogeographic inference and applied different post hoc approaches to analyse a new and comprehensive data set of viral genomes to elucidate the dispersal history and dynamics of rabies virus (RABV) in Iran, which have remained largely unknown. We first analysed the association between environmental factors and variations in dispersal velocity among lineages. Second, we present, test and apply a new approach to study the link between environmental conditions and the dispersal direction of lineages. The statistical performance (power of detection, false‐positive rate) of this new method was assessed using simulations. We performed phylogeographic analyses of RABV genomes, allowing us to describe the large diversity of RABV in Iran and to confirm the cocirculation of several clades in the country. Overall, we estimate a relatively high lineage dispersal velocity, similar to previous estimates for dog rabies virus spread in northern Africa. Finally, we highlight a tendency for RABV lineages to spread in accessible areas associated with high human population density. Our analytical workflow illustrates how phylogeographic approaches can be used to investigate the impact of environmental factors on several aspects of viral dispersal dynamics.

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Spatio‐temporal analysis of Nova virus, a divergent hantavirus circulating in the European mole in Belgium

Cited by 28 publications

References 80 publications

Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference — Application to H5N1 spread in the Mekong region

Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference — Application to H5N1 spread in the Mekong region

A Novel Hantavirus of the European Mole, Bruges Virus, Is Involved in Frequent Nova Virus Coinfections

Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages — Application to rabies virus spread in Iran

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