WILD-TYPE MEASLES VIRUSES WITH NON-STANDARD GENOME LENGTHS

Monday, 18th of August 2014

[source]PLoS One[|source]

The genetic characterization of circulating wild-type measles viruses is a critical component of laboratory surveillance for measles. In combination with standard case classification, virologic surveillance provides a sensitive means to describe the transmission pathways of measles virus. Virologic surveillance is required to document the interruption of transmission of endemic measles.

Measles viruses can be grouped into eight clades, subdivided into 24 genotypes based on the highly variable 450 nucleotides coding for the carboxyl-terminus of the nucleocapsid protein (N-450). However, N-450 does not always provide sufficient resolution to differentiate lineages within one genotype. Differentiation of co-circulating lineages within a genotype may require expansion of the size of the region of the genome used for sequence analysis. While there is a large amount of sequence data available for the nucleocapsid protein (N) and hemagglutinin (H) genes for all genotypes, much less information is available for other regions of the genome. 

 

While the standard length of the single stranded, measles virus is highly conserved at 15,894 nucleotides (nt), the authors in this study report the genomic sequences of 2 wild-type viral isolates of genotype D4 with genome lengths of 15,900 nt. The report documents a measles virus genome in which there is a 7 nucleotide insertion in the matrix gene and 1 nucleotide deletion in the fusion gene. More details are accessible at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991672/

 

ABSTRACT

The length of the single stranded, negative sense RNA genome of measles virus (MeV) is highly conserved at 15,894 nucleotides (nt). MeVs can be grouped into 24 genotypes based on the highly variable 450 nucleotides coding for the carboxyl-terminus of the nucleocapsid protein (N-450). Here, we report the genomic sequences of 2 wild-type viral isolates of genotype D4 with genome lengths of 15,900 nt. Both genomes had a 7 nt insertion in the 3′ untranslated region (UTR) of the matrix (M) gene and a 1 nt deletion in the 5 UTR of the fusion (F) gene. The net gain of 6 nt complies with the rule-of-six required for replication competency of the genomes of morbilliviruses. The insertions and deletion (indels) were confirmed in a patient sample that was the source of one of the viral isolates. The positions of the indels were identical in both viral isolates, even though epidemiological data and the 3 nt differences in N-450 between the two genomes suggested that the viruses represented separate chains of transmission. Identical indels were found in the M-F intergenic regions of 14 additional genotype D4 viral isolates that were imported into the US during 2007–2010. Viral isolates with and without indels produced plaques of similar size and replicated efficiently in A549/hSLAM and Vero/hSLAM cells. This is the first report of wild-type MeVs with genome lengths other than 15,894 nt and demonstrates that the length of the M-F UTR of wild-type MeVs is flexible.