The alphavirus 3'-nontranslated region: size heterogeneity and arrangement of repeated sequence elements

Virology
M PfefferO R Kaaden

Abstract

The 3'-nontranslated region (NTR) of representative strains of all known alphavirus species was amplified by reverse transcription-polymerase chain reaction. For 23 of them, the 3'-NTR sequence was determined. Together with previously published data, this allowed an analysis of the 3'-NTR of the viruses in the genus Alphavirus. The length of the 3'-NTRs varied from 77 nt for Pixuna virus to 609 nt for Bebaru virus. The 19-nt conserved sequence element directly adjacent to the poly(A) tract was found in all viruses, supporting the hypothesis that this region is a cis-acting sequence element during viral replication and essential for virus growth in vitro. Within the 3'-NTR of all alphaviruses, repeated sequence elements of various numbers and lengths were found. Their composition was very consistent in both the Venezuelan equine encephalitis (VEE) and the Sindbis-like viruses, although their number was constant only within the latter group. For the VEE viruses, our data suggested that insertion events rather than deletions from an ancestor with a long 3'-NTR created the various number of repeated sequence elements. Among the remaining viruses, both the number and the composition of repeated sequence elements varied remarkedly.

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Citations

Mar 26, 2002·Journal of Veterinary Medicine. B, Infectious Diseases and Veterinary Public Health·M PfefferR M Kinney
Dec 10, 1999·Journal of Virology·S VilloingM Brémont
Oct 3, 2001·Journal of Virology·A M PowersS C Weaver
Mar 30, 2005·Journal of Virology·Richard W Hardy, Charles M Rice
Jan 1, 2008·Wiener klinische Wochenschrift·Martin PfefferGerhard Dobler
Jan 30, 2015·Virus Research·Jennifer L HydeJeffrey Wilusz
Mar 31, 2015·Genome Announcements·Silke WölfelGerhard Dobler
Sep 8, 2009·Virology·Maxime SolignatChristian Devaux
Feb 28, 2017·Scientific Reports·Miguel Angel SanzLuis Carrasco
Feb 9, 2018·Viruses·Luis CarrascoEsther González-Almela
Aug 28, 2001·Proceedings. Biological Sciences·C R BrownM Pfeffer
Sep 1, 2019·Viruses·Adriano de Bernardi SchneiderMichael T Wolfinger
Nov 2, 2019·The Journal of General Virology·Kyra HermannsSandra Junglen
Feb 17, 2017·The Journal of General Virology·Kyra HermannsSandra Junglen
Jan 21, 2000·The Journal of General Virology·D J NetolitzkyL P Nagata
Apr 18, 2000·The Journal of General Virology·Y Shirako, Y Yamaguchi
Jul 16, 2020·Seminars in Cell & Developmental Biology·Claudia V FilomatoriDiego E Alvarez
Dec 22, 2020·Frontiers in Veterinary Science·Tongwei RenZuzhang Wei
Nov 6, 2020·Journal of Virology·Fernando MerwaissMaría-Carla Saleh
Jul 3, 2021·Pathogens·Autumn T LaPointe, Kevin J Sokoloski

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