Phylogenomic Signatures of a Lineage of Vesicular Stomatitis Indiana Virus Circulating During the 2019-2020 Epidemic in the United States
Por:
Zarate, S, Bertram, MR, Rodgers, C, Reed, K, Pelzel-McCluskey, A, Gomez-Romero, N, Rodriguez, LL, Mayo, C, Mire, C, Pond, SLK, Velazquez-Salinas, L
Publicada:
1 nov 2024
Resumen:
For the first time, we describe phylogenomic signatures of an epidemic lineage of vesicular stomatitis Indiana virus (VSIV). We applied multiple evolutionary analyses to a dataset of 87 full-length genome sequences representing the circulation of an epidemic VSIV lineage in the US between 2019 and 2020. Based on phylogenetic analyses, we predicted the ancestral relationship of this lineage with a specific group of isolates circulating in the endemic zone of Chiapas, Mexico. Subsequently, our findings indicate that the lineage diversified into at least four different subpopulations during its circulation in the US. We identified single nucleotide polymorphisms (SNPs) that differentiate viral subpopulations and assessed their potential relevance using comparative phylogenetic methods, highlighting the preponderance of synonymous mutations during the differentiation of these populations. Purifying selection was the main evolutionary force favoring the conservation of this epidemic phenotype, with P and G genes as the main drivers of the evolution of this lineage. Our analyses identified multiple codon sites under positive selection and the association of these sites with specific functional domains at P, M, G, and L proteins. Based on ancestral reconstruction analyses, we showed the potential relevance of some of the sites identified under positive selection to the adaptation of the epidemic lineage at the population level. Finally, using a representative group of viruses from Colorado, we established a positive correlation between genetic and geographical distances, suggesting that positive selection on specific codon positions might have favored the adaptation of different subpopulations to circulation in specific geographical settings. Collectively, our study reveals the complex dynamics that accompany the evolution of an epidemic lineage of VSIV in nature. Our analytical framework provides a model for conducting future evolutionary analyses. The ultimate goal is to support the implementation of an early warning system for vesicular stomatitis virus in the US, enabling early detection of epidemic precursors from Mexico.
Filiaciones:
Zarate, S:
Univ Autonoma Ciudad Mexico, Posgrad Ciencias Genom, Mexico City 03100, Mexico
Bertram, MR:
US Dept Agr, Agr Res Serv, Natl Bioand Agrodef Facil, Manhattan, KS 66506 USA
Rodgers, C:
Colorado State Univ, Dept Microbiol Immunol & Pathol, Ft Collins, CO 80523 USA
Reed, K:
Colorado State Univ, Dept Microbiol Immunol & Pathol, Ft Collins, CO 80523 USA
Pelzel-McCluskey, A:
US Dept Agr, Anim & Plant Hlth Inspection Serv, Vet Serv, Ft Collins, CO 80521 USA
Gomez-Romero, N:
Univ Nacl Autonoma Mexico, Fac Med Vet & Zootecnia, Dept Microbiol Inmunol, Ave Univ 3000 Col Copilco Univ, Mexico City 14510, Mexico
Rodriguez, LL:
US Dept Agr, Agr Res Serv, Natl Bioand Agrodef Facil, Manhattan, KS 66506 USA
Mayo, C:
Colorado State Univ, Dept Microbiol Immunol & Pathol, Ft Collins, CO 80523 USA
Mire, C:
US Dept Agr, Agr Res Serv, Natl Bioand Agrodef Facil, Manhattan, KS 66506 USA
Pond, SLK:
Temple Univ, Inst Genom & Evolutionary Med, Dept Biol, Philadelphia, PA 19122 USA
Velazquez-Salinas, L:
US Dept Agr, Agr Res Serv, Natl Bioand Agrodef Facil, Manhattan, KS 66506 USA
gold, All Open Access; Gold Open Access
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