title: Common position of indels that cause deviations from canonical genome organization in different measles virus strains.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: University of Zagreb, Centre for research and knowledge transfer in biotechnology, Rockefellerova 10, 10 000, Zagreb, Croatia. jivancic@unizg.hr.|Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia. jivancic@unizg.hr.
authors.forename: Jelena
authors.initials: J
authors.lastname: Ivancic-Jelecki
authors.affiliation: University of Zagreb, Centre for research and knowledge transfer in biotechnology, Rockefellerova 10, 10 000, Zagreb, Croatia.|Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia.
authors.forename: Anamarija
authors.initials: A
authors.lastname: Slovic
authors.affiliation: University of Zagreb, Centre for research and knowledge transfer in biotechnology, Rockefellerova 10, 10 000, Zagreb, Croatia.|Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia.
authors.forename: Maja
authors.initials: M
authors.lastname: Šantak
authors.affiliation: Pediatric infectious diseases department, University hospital for infectious diseases "Dr. Fran Mihaljevic", Mirogojska 8, 10 000, Zagreb, Croatia.
authors.forename: Goran
authors.initials: G
authors.lastname: Tešović
authors.affiliation: University of Zagreb, Centre for research and knowledge transfer in biotechnology, Rockefellerova 10, 10 000, Zagreb, Croatia.|Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia.
authors.forename: Dubravko
authors.initials: D
authors.lastname: Forcic
mesh_terms: D001483:Base Sequence; D016679:Genome, Viral; D005838:Genotype; D006801:Humans; D054643:INDEL Mutation; D008457:Measles / Q000821:virology*; D008459:Measles virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D010802:Phylogeny
keywords: Genome editing; Genome organization; Indels; M-F UTR; Measles virus; Mononucleotide repeats; Non-canonical strains; Prolonged genome