Effective molecular surveillance of measles virus during measles elimination
| dc.contributor.author | Schulz, Helene | |
| dc.contributor.examiningcommittee | Embree, Joanne (Medical Microbiology & Infectious Diseases) | en_US |
| dc.contributor.examiningcommittee | Graham, Morag (Medical Microbiology & Infectious Diseases) | en_US |
| dc.contributor.examiningcommittee | Hausner, Georg (Microbiology) | en_US |
| dc.contributor.examiningcommittee | Griffin, Dianne (Johns Hopkins Bloomberg School of Public Health) | en_US |
| dc.contributor.supervisor | Severini, Alberto (Medical Microbiology & Infectious Diseases) | en_US |
| dc.date.accessioned | 2020-04-03T20:53:36Z | |
| dc.date.available | 2020-04-03T20:53:36Z | |
| dc.date.copyright | 2020-04-03 | |
| dc.date.issued | 2020-02-14 | en_US |
| dc.date.submitted | 2020-04-01T16:48:27Z | en_US |
| dc.date.submitted | 2020-04-03T20:33:40Z | en_US |
| dc.degree.discipline | Medical Microbiology and Infectious Diseases | en_US |
| dc.degree.level | Doctor of Philosophy (Ph.D.) | en_US |
| dc.description.abstract | Measles virus (MeV) is a highly infectious virus and the causative agent of measles disease. Despite the availability of a safe and cost-effective vaccine, measles is one of the world-leading causes of death in young children. Endemic circulation of the Measles virus in Canada has been interrupted since 1998 and all cases result from importation from endemic areas. The ongoing global elimination efforts have contributed to the decreasing diversity of MeV genome, creating difficulty in distinguishing independent importation of MeV from local transmission when relying only on the WHO recommended genotyping targets, the 450nt region of the C-terminus of the N gene, and the additional 1854nt H gene. Traceability of measles cases in outbreaks is essential to document MeV elimination status. A higher-resolution genotyping method or MeV whole genome sequencing (WGS) has been advocated by the World Health Organization (WHO) as the approach needed to overcome the current difficulty in resolving the decreasing diversity of MeV isolates. I applied WGS by Sanger and Illumina next generation sequencing (NGS) and extended genotyping to several Canadian and Brazilian outbreaks from 2011 to 2015, with the purposes of developing a WGS method that could be applied directly and efficiently to clinical specimens, sequencing the entire genome of MeV isolates from recent Canadian and international outbreaks, to determine the rate of variation of MeV genomes during transmission, identifying hypervariable genome regions and their ability to serve as a surrogate of WGS for distinguishing MeV isolates, establishing the minimum number of substitutions that could distinguish direct transmission from independent importations of similar viruses, and calculating the clock rate of MeV during transmission by using the dates of rash onset of the outbreak isolates and developing a strategy with Bayesian Evolutionary Analysis of Sampling Trees (BEAST) to distinguish chains of transmissions from endemic transmission. My results show that the non-coding region between matrix and fusion gene (MF-NCR) is very sensitive in distinguishing separate importation events from local transmission. Based on WGS, this region accounts for most of the variability of MeV isolates originating from the same outbreak. The MF-NCR is also receptive to insertions and deletions (INDELs) and their unique presentation, if present, enables outbreak resolution. WGS and extended genotyping of the MFNCR target will empower epidemiological investigation as global measles elimination is approached, and the diversity of the measles genome decreases. BEAST analysis of this outbreak revealed a clock rate of about 3.11E-3 and 5.40E-4 substitutions per site per year for the MF-NCR and the whole genome, respectively. Applying the BEAST algorithm to a real-world scenario leads to the conclusion that a two-nucleotide difference in the measles genome of concurrently circulating strains makes direct transmission unlikely and supports the hypothesis of an independent importation of MeV. Since the MeV genome changes very slowly during outbreaks, unlike other RNA viruses, the WHO-standardized regions on N and H gene are not diverse enough to discriminate between different importations events during outbreaks. I demonstrated that the MF-NCR high-resolution genotyping target satisfactorily allows effective molecular surveillance during measles elimination, filling the gap between epidemiological contact tracing and molecular surveillance, while some scenarios need to be evaluated with WGS, which will become a gold-standard as more WHO regions approach MeV elimination. | en_US |
| dc.description.note | May 2020 | en_US |
| dc.identifier.uri | http://hdl.handle.net/1993/34633 | |
| dc.language.iso | eng | en_US |
| dc.rights | open access | en_US |
| dc.subject | Measles Virus | en_US |
| dc.subject | MeV | en_US |
| dc.subject | BEAST (Bayesian Evolutionary Analsysis of Sampling Trees) | en_US |
| dc.subject | Molecular surveillance | en_US |
| dc.subject | WGS | en_US |
| dc.subject | NGS | en_US |
| dc.subject | MF-NCR | en_US |
| dc.subject | clock rate | en_US |
| dc.title | Effective molecular surveillance of measles virus during measles elimination | en_US |
| dc.type | doctoral thesis | en_US |