Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks

Abstract

BackgroundMeasles is a highly infectious disease caused by measles virus (MeV). Despite the availability of a safe and cost-effective vaccine, measles is one of the world-leading causes of death in young children. Within Europe, there is a target for eliminating endemic measles in 2015, with molecular epidemiology required on 80% of cases for inclusion/exclusion of outbreak transmission chains. Currently, MeV is genotyped on the basis of a 450 nucleotide region of the nucleoprotein gene (N-450) and the hemagglutinin gene (H). However, this is not sufficiently informative for distinguishing endemic from imported MeV. We have developed an amplicon-based method for obtaining whole genome sequences (WGS) using NGS or Sanger methodologies from cell culture isolates or oral fluid specimens, and have sequenced over 60 samples, including 42 from the 2012 outbreak in the UK.ResultsOverall, NGS coverage was over 90% for approximately 71% of the samples tested. Analysis of 32 WGS excluding 3’ and 5’ termini (WGS-t) obtained from the outbreak indicates that the single nucleotide difference found between the two major groups of N-450 sequences detected during the outbreak is most likely a result of stochastic viral mutation during endemic transmission rather than of multiple importation events: earlier strains appear to have evolved into two distinct strain clusters in 2013, one containing strains with both outbreak-associated N-450 sequences. Additionally, phylogenetic analysis of each genomic region of MeV for the strains in this study suggests that the most information is acquired from the non-coding region located between the matrix and fusion protein genes (M/F NCR) and the N-450 genotyping sequence, an observation supported by entropy analysis across genotypes.ConclusionsWe suggest that both M/F NCR and WGS-t could be used to complement the information from classical epidemiology and N-450 sequencing to address specific questions in the context of measles elimination.

Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples

“…SAMtools v1.4 was used to compute the percent reads mapped and coverage depth (34). Mapping consensuses for Illumina sequencing were generated using QuasiBam (40). Maximum likelihood phylogeny was generated for the HA gene segment using RAxML v8.2.10 (41), in which a general time-reversible model of nucleotide substitution and a gamma-distributed rate variation among sites were applied.…”

Future research to underpin successful peste des petits ruminants virus (PPRV) eradication

“…Logically, however, it may be beneficial to plan strategically for entire genome sequencing, to allow detailed monitoring of any ongoing PPRV epidemic. This genome-wide approach was shown recently to be essential for identifying the origin of a measles outbreak at the 2010 Vancouver Winter Olympic Games [76][77][78]; furthermore, full PPRV genome sequences, including vaccine sequences, are already available to support this effort [79,80] (Table 1 and Fig. 2).…”

Seroprevalence and Risk Factors Associated with Measles outbreaks among Children in Kwale, Lamu and Narok Counties in Kenya, 2014

“…Our results suggest that the general population sero -immunity among children between 9 to 59 months as in 2014, was 83.0%, well below the acceptable herd immunity threshold (93-95%) necessary to interrupt measles transmission as suggested by several studies [14,19,32]. Comparatively, this is much higher than what another recent (2011) study in Bangui, Central African Republic (CAR) found (57.3 %) on a research conducted in 2008 despite having reached immunization coverage's of more than 90% in 2006 [34].…”

“…Such association has been emphasized by world health organization [19,36,37]. And mentioned in reports from other studies as well [14,20,38]. The odds of being seronegative were higher for residents of Narok County as compared to Kwale or Lamu counties.…”

“…This prompted a massive immunisation programme that covered more than 99% of the target population (9 -59 months old children) [11][12][13]. Genetic characterisation of measles virus has revealed 24 genotypes distributed within 8 genotypic groups as; A, B1-3, C1-2, D1-11, E, F, G1-3, and H1-2 [14]. Phenotypically, measles virus is mono topic; hence we have only one serotype [15].…”