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In this study, we demonstrate that differences within the P2 domain of norovirus genogroup I (GI) strains can be used to segregate outbreaks which are unrelated, whereas complete conservation within this region allows tracking of strains that are part of a single outbreak and likely to have a common source.

The aim of this study was to apply sequence analysis of a hyper variable region of the norovirus (NoV) genome in order to identify point source outbreaks associated with suspect food or water. The hyper-variable region of the gene encoding the P2 domain was chosen as small differences in sequence are likely to indicate virus from different sources whereas identical sequence may reveal transmission routes and the source of contamination. Strains with 100% similarity were considered as originating from a common source, whereas, strains with one or more mutations in the hyper variable region sequenced were regarded as representing unrelated transmission events. This study was able to identify a point source outbreak of a dominant strain, GII-4, on a cruise ship but also of a less common strain, GII-2, between two schools. Also identical GII-3 strains were demonstrated in food handlers amongst the same outbreak; however epidemiologically related outbreaks showed different GII-3 strains indicating multiple sources of contamination., (Copyright 2009 Wiley-Liss, Inc.)

Tracking the spread of noroviruses during outbreaks of gastroenteritis is hampered by the lack of sequence diversity in those regions of the genome chosen for virus detection and characterization. Sequence analysis of regions of the genes encoding the RNA-dependent RNA polymerase and the S domain of the capsid does not provide sufficient discrimination between genotypically related strains of different outbreaks. However, analysis of sequences derived from the region encoding the P2 domain showed 100% similarity among strains from the same outbreak and <100% similarity among strains of different outbreaks. The prolonged nature of some hospital outbreaks, links between hospitals, and the introduction of multiple strains of a single genotype associated with an outbreak aboard a cruise ship were determined using this method. This provides a powerful tool for tracking outbreak strains and the subsequent analysis and validation of interventions in a background of multiple introductions of virus strains of the same genotype or genetic cluster.

Streptococcus pyogenes strains were genotyped by a combination of molecular methods for high- resolution epidemiologic studies of disease outbreaks. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the emm gene is reported. Alone or in conjunction with other molecular techniques (16S ribotyping, pulsed-field gel electrophoresis, and detection of exotoxin genes), PCR-RFLP could differentiate outbreak-related strains from contemporaneous background strains of the same M serotype. Three outbreaks were studied: pharyngitis in a boarding school (serotype M5), cross-infection in a hospital burn unit (serotype M76), and severe invasive disease in two elderly care homes (serotype R28). It was possible, for example, to identify within serotype R28 a clone with particular potential for invasive disease. In all cases, the four molecular methods yielded complementary results that were hierarchically related. Strains could be assigned to the outbreak or the background in a precise, reproducible, and rapid manner.