Common position of indels that cause deviations from canonical genome organization in different measles virus strains

Scientific paper - Original scientific paper

• Author: Jelena Ivančić-Jelečki
• Author: Anamarija Slović
• Author: Maja Šantak
• Author: Goran Tešović
• Author: Dubravko Forčić
• Author's institution: University of Zagreb; School of Medicine
• Scientific / art field, discipline and subdiscipline: BIOMEDICINE AND HEALTHCARE; Clinical Medical Sciences

Abstract (english)

BACKGROUND:

The canonical genome organization of measles virus (MV) is characterized by total size of 15 894 nucleotides (nts) and defined length of every genomic region, both coding and non-coding. Only rarely have reports of strains possessing non-canonical genomic properties (possessing indels, with or without the change of total genome length) been published. The observed mutations are mutually compensatory in a sense that the total genome length remains polyhexameric. Although programmed and highly precise pseudo-templated nucleotide additions during transcription are inherent to polymerases of all viruses belonging to family Paramyxoviridae, a similar mechanism that would serve to non-randomly correct genome length, if an indel has occurred during replication, has so far not been described in the context of a complete virus genome. -----

METHODS:

We compiled all complete MV genomic sequences (64 in total) available in open access sequence databases. Multiple sequence comparisons and phylogenetic analyses were performed with the aim of exploring whether non-recombinant and non-evolutionary linked measles strains that show deviations from canonical genome organization possess a common genetic characteristic. -----

RESULTS:

In 11 MV sequences we detected deviations from canonical genome organization due to short indels located within homopolymeric stretches or next to them. In nine out of 11 identified non-canonical MV sequences, a common feature was observed: one mutation, either an insertion or a deletion, was located in a 28 nts long region in F gene 5' untranslated region (positions 5051-5078 in genomic cDNA of canonical strains). This segment is composed of five tandemly linked homopolymeric stretches, its consensus sequence is G6-7C7-8A6-7G1-3C5-6. Although none of the mononucleotide repeats within this segment has fixed length, the total number of nts in canonical strains is always 28. These nine non-canonical strains, as well as the tenth (not mutated in 5051-5078 segment), can be grouped in three clusters, based on their passage histories/epidemiological data/genetic similarities. There are no indications that the 3 clusters are evolutionary linked, other than the fact that they all belong to clade D. -----

CONCLUSIONS:

A common narrow genomic region was found to be mutated in different, non-related, wild type strains suggesting that this region might have a function in non-random genome length corrections occurring during MV replication.

• Keywords (english): Base Sequence; Genome, Viral; Genotype; Humans; INDEL Mutation; Measles/virology; Measles virus/classification; Measles virus/genetics; Measles virus/isolation & purification; Molecular Sequence Data; Phylogeny
• Language: english
• Publication type: Scientific paper - Original scientific paper
• Publication status: Published
• Peer review: Peer review
• Publication version: Published version
• Journal title: Virology Journal
• Numbering: vol. 13, no. 1, p. 134
• p-ISSN: 1743-422X
• DOI: https://doi.org/10.1186/s12985-016-0587-2
• URN:NBN: urn:nbn:hr:105:393633
• Publication: 2016-07-29
• Document URL: https://doi.org/10.1186/s12985-016-0587-2
• Type of resource: Text
• Access conditions: Open access
• Created on: 2024-03-28 08:47:51