P2 domain profiles and shedding dynamics in prospectively monitored norovirus outbreaks

Sukhrie, Faizel H. A.; Teunis, Peter; Vennema, Harry; Bogerman, Jolanda; Marm, Sebastian van; Beersma, Matthias F. C.

doi:10.1016/j.jcv.2012.12.006

Cited by 22 publications

(21 citation statements)

References 23 publications

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“…P2 sequences have been used to trace norovirus outbreaks in hospitals and nursing homes (18)(19)(20)35), as well as to establish the number of mutations over the course of a norovirus infection (20). Within an outbreak, sequence diversity between subjects is small (0 to 0.3%); however, viruses collected later in an infection of the same person accumulated several mutations, compared to viruses shed at the onset of the infection (20). P2 sequence data for the GI.6 outbreaks in our study differed 0 to 2%, which could indicate that at least several outbreaks might have had a common source or, alternatively, had minimal circulation.…”

Section: Epidemiologic Characteristics Of Norovirus Outbreaks In Thementioning

confidence: 99%

Genotypic and Epidemiologic Trends of Norovirus Outbreaks in the United States, 2009 to 2013

et al. 2014

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In addition, three non-GII.4 viruses, i.e., GII.12, GII.1, and GI.6, caused 528 (13%) of all outbreaks. Several non-GII.4 genotypes (GI.3, GI.6, GI.7, GII.3, GII.6, and GII.12) were significantly more associated with food-borne transmission (odds ratio, 1.9 to 7.1; P < 0.05). Patients in LTCF and people >65 years of age were at higher risk for GII.4 infections than those in other settings and with other genotypes (P < 0.05). Phylogeographic analysis identified three major dispersions from two geographic locations that were responsible for the GI.6 outbreaks from 2011 to 2013. In conclusion, our data demonstrate the cyclic emergence of new (non-GII.4) norovirus strains, and several genotypes are more often associated with food-borne outbreaks. These surveillance data can be used to improve viral food-borne surveillance and to help guide studies to develop and evaluate targeted prevention methods such as norovirus vaccines, antivirals, and environmental decontamination methods.

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Section: Epidemiologic Characteristics Of Norovirus Outbreaks In Thementioning

confidence: 99%

Genotypic and Epidemiologic Trends of Norovirus Outbreaks in the United States, 2009 to 2013

et al. 2014

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“…Accordingly, public health measures to identify and eliminate sources of infection or behavior leading to virus spread are warranted (17, 18). The utility of viral sequencing to track norovirus in transmission studies has been explored with fragments of the viral genome (19–22). As a consequence of the speed of disease onset and high transmissibility, the number of nucleotide and amino acid sequence changes within a local outbreak may be rare, so the sequencing of larger genomic fragments should provide greater resolution for defining transmission patterns.…”

Section: Introductionmentioning

confidence: 99%

Deep Sequencing of Norovirus Genomes Defines Evolutionary Patterns in an Urban Tropical Setting

Cotten

Petrova

Phan

et al. 2014

J Virol

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Norovirus is a highly transmissible infectious agent that causes epidemic gastroenteritis in susceptible children and adults. Norovirus infections can be severe and can be initiated from an exceptionally small number of viral particles. Detailed genome sequence data are useful for tracking norovirus transmission and evolution. To address this need, we have developed a whole-genome deep-sequencing method that generates entire genome sequences from small amounts of clinical specimens. This novel approach employs an algorithm for reverse transcription and PCR amplification primer design using all of the publically available norovirus sequence data. Deep sequencing and de novo assembly were used to generate norovirus genomes from a large set of diarrheal patients attending three hospitals in Ho Chi Minh City, Vietnam, over a 2.5-year period. Positive-selection analysis and direct examination of protein changes in the virus over time identified codons in the regions encoding proteins VP1, p48 (NS1-2), and p22 (NS4) under positive selection and expands the known targets of norovirus evolutionary pressure.IMPORTANCE The high transmissibility and rapid evolutionary rate of norovirus, combined with a short-lived host immune responses, are thought to be the reasons why the virus causes the majority of pediatric viral diarrhea cases. The evolutionary patterns of this RNA virus have been described in detail for only a portion of the virus genome and never for a virus from a detailed urban tropical setting. We provide a detailed sequence description of the noroviruses circulating in three Ho Chi Minh City hospitals over a 2.5-year period. This study identified patterns of virus change in known sites of host immune response and identified three additional regions of the virus genome under selection that were not previously recognized. In addition, the method described here provides a robust full-genome sequencing platform for community-based virus surveillance.

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“…These methods have been useful in outbreak investigation, especially in determining whether an accumulation of NoV cases is composed of several different genotypes, likely reflecting individual introductions and sometimes called a pseudo outbreak [ 23 ]. However, sequencing of longer parts of the capsid gene, especially the hypervariable P2 domain, provides more detailed information and has recently been used to study transmission routes [ 24 – 28 ]. Whole genome sequencing using next generation sequencing technology has also proved feasible and useful in outbreak investigation [ 29 ].…”

Section: Introductionmentioning

confidence: 99%

Sequence Analysis of the Capsid Gene during a Genotype II.4 Dominated Norovirus Season in One University Hospital: Identification of Possible Transmission Routes

et al. 2015

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Norovirus (NoV) is a leading cause of gastroenteritis and genotype II.4 (GII.4) is responsible for the majority of nosocomial NoV infections. Our objective was to examine whether sequencing of the capsid gene might be a useful tool for the hospital outbreak investigation to define possible transmission routes. All NoV positive samples submitted from one university hospital during the 2007/8 season were selected. Genotyping of selected samples by partial polymerase gene sequencing had shown that the majority belonged to the GII.4 variant Den Haag 2006b and had identical polymerase sequences. Sequences of the capsid gene (1412 nucleotides) were obtained from the first available sample from 55 patients. From six immunocompromised patients with persistent infections a second sample was also included. As a control for a point-source outbreak, five samples from a foodborne outbreak caused by the same GII.4 variant were analyzed. Forty-seven of the inpatients (85%) were infected with the GII.4 variant Den Haag 2006b. Phylogenetic analysis of the Den Haag 2006b sequences identified four distinct outbreaks in different departments and a fifth outbreak with possible inter-department spread. In addition, a more heterogeneous cluster with evidence of repeated introductions from the community, but also possible inter-department spread was observed. In all six patients with paired sequences, evidence for in vivo evolution of the virus was found. Capsid gene sequencing showed substantial sequence variation among NoV GII.4 variant Den Haag 2006b strains from one single institution during a nine months’ period. This method proved useful to understand the local epidemiology and, when used promptly, has the potential to make infection control measures more targeted.

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P2 domain profiles and shedding dynamics in prospectively monitored norovirus outbreaks

Cited by 22 publications

References 23 publications

Genotypic and Epidemiologic Trends of Norovirus Outbreaks in the United States, 2009 to 2013

Genotypic and Epidemiologic Trends of Norovirus Outbreaks in the United States, 2009 to 2013

Deep Sequencing of Norovirus Genomes Defines Evolutionary Patterns in an Urban Tropical Setting

Sequence Analysis of the Capsid Gene during a Genotype II.4 Dominated Norovirus Season in One University Hospital: Identification of Possible Transmission Routes

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