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. 2022 Jun;53(2):1065-1075.
doi: 10.1007/s42770-022-00724-2. Epub 2022 Apr 8.

Phylodynamics of classical swine fever virus in Brazil

Antônio Augusto Fonseca Júnior  1   2 , Mateus Laguardia-Nascimento  3 , Aline Aparecida Silva Barbosa  3 , Valdenia Lopes da Silva Gonçalves  3 , Tânia Rosária Pereira Freitas  3 , Anselmo Vasconcelos Rivetti Júnior  3 , Marcelo Fernandes Camargos  3
Affiliations

Phylodynamics of classical swine fever virus in Brazil

Antônio Augusto Fonseca Júnior et al. Braz J Microbiol. 2022 Jun.

Abstract

The classical swine fever virus is the etiologic agent of one of the diseases with the greatest impact on swine farming worldwide. An extensive area of Brazil is considered free of the disease, but some states in Northeast Brazil have registered outbreaks since 2001. The objective of this study was to analyze the genetic variations of the virus and its spread over time and space. Partial sequences of the viral E2 protein obtained from samples collected during the Brazilian outbreaks were compared with sequences from the GenBank database (NCBI). The results demonstrated the continuous presence of the virus in the state of Ceará, with diffusion to at least two other states. The Brazilian Northeast virus presents specific polymorphisms that separate it from viruses isolated in other countries.

Keywords: Classical swine fever; Evolution; Hog cholera; Phylogeny.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Municipalities from CE and PI where CSF outbreaks increased between 2018 and 2020. CE (number of outbreaks): Forquilha (2), Groaíras (6), Santa Quitéria (2), Varjota (3), Reriutaba (4), Cariré (6), Moraujo (4), Frecheirinha (3), Mulungu (1), Graça (1), Ipu (1), Hidrolândia (1), Martinópole (1), Tianguá (2), Coreaú (2), Sobral (1), Croatá (2), Granja (3), Viçosa do Ceará (2), Massapê (1). PI: Lagoa do Piauí (2), Cabeceiras do Piauí (5), Murici dos Portelas (4), Domingos Mourão (2), Brasileira (2), Milton Brandão (1), São João do Arraial (1), Parnaíba, (1), Luís Correia (1)
Fig. 2
Fig. 2
Phylogenetic tree built using MEGA X, the K2 model of nucleotide substitution, and the Maximum Likelihood model with 1000 replicas of bootstraps
Fig. 3
Fig. 3
Bayesian skyline reconstruction from the data generated using Beast 2.0 for subgenotype 1.5 samples. The result indicates a steady population with a slight increase from 2018 onwards
Fig. 4
Fig. 4
Phylogeographic analysis of samples of sub genotype 1.5 collected in foci of Northeast Brazil. The data demonstrate the spread of the virus in CE and its subsequent spread to PI and RN
Fig. 5
Fig. 5
Phylogenetic network generated in PopArt by the Median Joining Network model for samples from Brazil and other countries. The circles show the Brazilian samples of the subgenotype 1.5. The results demonstrate the clear separation of samples from recent outbreaks and those detected in the early 2000s in the Brazilian Northeast
Fig. 6
Fig. 6
Phylogenetic network generated in PopArt by the Median Joining Network model for Brazilian samples only. The circles were colored by state. The results demonstrate the genetic difference between the sequences of the states of AP, MA, and RN. The sequences of outbreaks from 2018 are phylogenetically closer to those that caused the outbreaks between 2001 and 2009 in the state of CE
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