Phylogenetic and phylodynamic analysis of a classical swine fever virus outbreak in Japan (2018-2020).
BEAST
Japan
classical swine fever (CSF)
most recent common ancestor
phylogenetic analysis
phylogeographic analysis
Journal
Transboundary and emerging diseases
ISSN: 1865-1682
Titre abrégé: Transbound Emerg Dis
Pays: Germany
ID NLM: 101319538
Informations de publication
Date de publication:
May 2022
May 2022
Historique:
revised:
12
04
2021
received:
01
02
2021
accepted:
16
04
2021
pubmed:
24
4
2021
medline:
7
5
2022
entrez:
23
4
2021
Statut:
ppublish
Résumé
After 26 years, another classical swine fever virus (CSFV) outbreak in domestic pigs and wild boars occurred in Japan 2018. Herein, we investigated the entry and the spatial dynamics of the CSFV outbreak in Japan using the nearly complete genomes of strains isolated from both wild boars and domestic pigs during this epidemic. Phylogenetic analysis showed that the most recent common ancestor (MRCA) of the Japanese lineage emerged 146 days (95% highest posterior density (HPD): 85-216 days) before the index case was detected. Based on epidemiological analysis, the period for the 95% HPD was 1 month earlier than the time of virus introduction into the index farm. The disease mainly spreads to the adjoining regions during the epidemic, with no spread to the nonadjacent regions. This result indicates that human activities, such as the movement of vehicles, contributed to the infection spread. As cases occurred in nonadjacent regions, the MRCA for the epidemic in the Saitama prefecture was estimated to have emerged 93 days before the date of detection in the initial farm in this region. Similarly, the MRCA for the epidemic in Okinawa prefecture, more than 1,300 km away from the other infected regions, was estimated to have emerged 34 days before the date of detection in the region's primary farm. Therefore, our results indicate that if exotic diseases emerge after a long period of absence or in a disease-free country, a longer period of time will elapse before detection, resulting in further spread. Additionally, subsequent infections occurring in regions distant from the original infected region will require less time for detection than in the original region. This study provides valuable insights into a CSFV outbreak that occurred in a previously CSFV-free country and thus beneficial in enhancing producers' awareness and allow for better preparation for infections.
Banques de données
GENBANK
['MG387218']
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1529-1538Subventions
Organisme : Ministry of Agriculture, Forestry and Fisheries
ID : JPJ008617
Organisme : Ministry of Agriculture, Forestry and Fisheries
ID : 20319390
Informations de copyright
© 2021 Wiley-VCH GmbH.
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