Dataset Information

Comprehensive phylogeographic and phylodynamic analyses of global Senecavirus A.

ABSTRACT: Senecavirus A (SVA) is a member of the genus Senecavirus in the family Picornaviridae that infects pigs and shows symptoms similar to foot and mouth diseases and other vesicular diseases. It is difficult to prevent, thus, causing tremendous economic loss to the pig industry. However, the global transmission routes of SVA and its natural origins remain unclear. In this study, we processed representative SVA sequences from the GenBank database along with 10 newly isolated SVA strains from the field samples collected from our lab to explore the origins, population characteristics, and transmission patterns of SVA. The SVA strains were firstly systematically divided into eight clades including Clade I-VII and Clade Ancestor based on the maximum likelihood phylogenetic inference. Phylogeographic and phylodynamics analysis within the Bayesian statistical framework revealed that SVA originated in the United States in the 1980s and afterward spread to different countries and regions. Our analysis of viral transmission routes also revealed its historical spread from the United States and the risk of the global virus prevalence. Overall, our study provided a comprehensive assessment of the phylogenetic characteristics, origins, history, and geographical evolution of SVA on a global scale, unlocking insights into developing efficient disease management strategies.

SUBMITTER: Gao H

PROVIDER: S-EPMC9557172 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Comprehensive phylogeographic and phylodynamic analyses of global Senecavirus A.

Gao Han H Chen Yong-Jie YJ Xu Xiu-Qiong XQ Xu Zhi-Ying ZY Xu Si-Jia SJ Xing Jia-Bao JB Liu Jing J Zha Yun-Feng YF Sun Yan-Kuo YK Zhang Gui-Hong GH

Frontiers in microbiology 20220929

Senecavirus A (SVA) is a member of the genus <i>Senecavirus</i> in the family Picornaviridae that infects pigs and shows symptoms similar to foot and mouth diseases and other vesicular diseases. It is difficult to prevent, thus, causing tremendous economic loss to the pig industry. However, the global transmission routes of SVA and its natural origins remain unclear. In this study, we processed representative SVA sequences from the GenBank database along with 10 newly isolated SVA strains from t ...[more]

PMID: 36246286

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Project description:BackgroundSince 1982, HIV-1 epidemics have evolved to different scenarios in terms of transmission routes, subtype distribution and characteristics of transmission clusters. We investigated the evolutionary history of HIV-1 subtype B in south Spain.Patients & methodsWe studied all newly diagnosed HIV-1 subtype B patients in East Andalusia during the 2005-2012 period. For the analysis, we used the reverse transcriptase and protease sequences from baseline resistance, and the Trugene® HIV Genotyping kit (Siemens, Barcelona, Spain). Subtyping was done with REGA v3.0. The maximum likelihood trees constructed with RAxML were used to study HIV-1 clustering. Phylogeographic and phylodynamic profiles were studied by Bayesian inference methods with BEAST v1.7.5 and SPREAD v1.0.6.ResultsOf the 493 patients infected with HIV-1 subtype B, 234 grouped into 55 clusters, most of which were small (44 clusters ≤ 5 patients, 31 with 2 patients, 13 with 3). The rest (133/234) were grouped into 11 clusters with ≥ 5 patients, and most (82%, 109/133) were men who have sex with men (MSM) grouped into 8 clusters. The association with clusters was more frequent in Spanish (p = 0.02) men (p< 0.001), MSM (p<0.001) younger than 35 years (p = 0.001) and with a CD4+ T-cell count above 350 cells/ul (p<0.001). We estimated the date of HIV-1 subtype B regional epidemic diversification around 1970 (95% CI: 1965-1987), with an evolutionary rate of 2.4 (95%CI: 1.7-3.1) x 10-3 substitutions/site/year. Most clusters originated in the 1990s in MSMs. We observed exponential subtype B HIV-1 growth in 1980-1990 and 2005-2008. The most significant migration routes for subtype B went from inland cities to seaside locations.ConclusionsWe provide the first data on the phylodynamic and phylogeographic profiles of HIV-1 subtype B in south Spain. Our findings of transmission clustering among MSMs should alert healthcare managers to enhance preventive measures in this risk group in order to prevent future outbreaks.

Project description:Recurrent outbreaks of senecavirus A (SVA)-associated vesicular disease have led to a large number of infected pigs being culled and has caused considerable economic losses to the swine industry. Although SVA was discovered 2 decades ago, knowledge about the evolutionary and transmission histories of SVA remains unclear. Herein, we performed an integrated analysis of the recombination, phylogeny, selection, and spatiotemporal dynamics of SVA. Phylogenetic analysis demonstrated that SVA diverged into two main branches, clade I (pre-2007 strains) and clade II (post-2007 strains). Importantly, analysis of selective strength showed that clade II was evolving under relaxed selection compared with clade I. Positive selection analysis identified 27 positive selective sites, most of which are located on the outer surface of capsid protomer or on the important functional domains of nonstructure proteins. Bayesian phylodynamics suggested that the estimated time to the most recent common ancestor of SVA was around 1986, and the estimated substitution rate of SVA was 3.3522 × 10-3 nucleotide substitutions/site/year. Demographic history analysis revealed that the effective population size of SVA has experienced a gradually increasing trend with slight fluctuation until 2017 followed by a sharp decline. Notably, Bayesian phylogeographic analysis inferred that Brazil might be the source of SVA's global transmission since 2015. In summary, these data illustrated that the ongoing evolution of SVA drove the lineage-specific innovation and potentially phenotypically important variation. Our study sheds new light on the fundamental understanding of SVA evolution and spread history. IMPORTANCE Recurrent outbreaks and global epidemics of senecavirus A-associated vesicular disease have caused heavy economic losses and have threatened the development of the pig industry. However, the question of where the virus comes from has been one of the biggest puzzles due to the stealthy nature of the virus. Consequently, tracing the source, evolution, and transmission pattern of SVA is a very challenging task. Based on the most comprehensive analysis, we revealed the origin time, rapid evolution, epidemic dynamics, and selection of SVA. We observed two main genetic branches, clade I (pre-2007 strains) and clade II (post-2007 strains), and described the epidemiological patterns of SVA in different countries. We also first identified Brazil as the source of SVA's global transmission since 2015. Findings in this study provide important implications for the control and prevention of the virus.

Dataset Information

Comprehensive phylogeographic and phylodynamic analyses of global Senecavirus A.

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Comprehensive phylogeographic and phylodynamic analyses of global Senecavirus A.

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