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Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History

Li, YQ; Bletsa, M; Zisi, Z; Boonen, I; Gryseels, S; Kafetzopoulou, L; Webster, JP; Catalano, S; Pybus, OG; Van de Perre, F; Li, HT; Li, YY; Li, YC; Abramov, A; Lymberakis, P; Lemey, P; Lequime, S

Authors

YQ Li

M Bletsa

Z Zisi

I Boonen

S Gryseels

L Kafetzopoulou

JP Webster

S Catalano

OG Pybus

F Van de Perre

HT Li

YY Li

YC Li

A Abramov

P Lymberakis

P Lemey

S Lequime



Abstract

As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large data set of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.

Citation

Li, Y., Bletsa, M., Zisi, Z., Boonen, I., Gryseels, S., Kafetzopoulou, L., Webster, J., Catalano, S., Pybus, O., Van de Perre, F., Li, H., Li, Y., Li, Y., Abramov, A., Lymberakis, P., Lemey, P., & Lequime, S. (2022). Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History. Molecular Biology and Evolution, 39(10), https://doi.org/10.1093/molbev/msac190

Journal Article Type Article
Acceptance Date Aug 23, 2022
Online Publication Date Sep 6, 2022
Publication Date 2022
Deposit Date Aug 11, 2023
Publicly Available Date Aug 11, 2023
Print ISSN 0737-4038
Electronic ISSN 1537-1719
Publisher Oxford University Press
Peer Reviewed Peer Reviewed
Volume 39
Issue 10
DOI https://doi.org/10.1093/molbev/msac190
Keywords endogenous viral element; pestivirus; Flaviviridae; Crocidura; host range; paleovirology; AMINO-ACID SITES; CROCIDURA; VIRUSES; FLAVIVIRUS; SEQUENCES; MAMMALIA; SORICIDAE; EVOLUTION; ALIGNMENT; PATTERNS

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