Characterizing Norovirus Transmission from Outbreak Data, United States.
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ABSTRACT:
SUBMITTER: Steele MK
PROVIDER: S-EPMC7392428 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundClinically, human immunodeficiency virus type 1 (HIV-1) pol sequences are used to evaluate for drug resistance. These data can also be used to evaluate transmission networks and help describe factors associated with transmission risk.MethodsHIV-1 pol sequences from participants at 5 sites in the CFAR Network of Integrated Clinical Systems (CNICS) cohort from 2000-2009 were analyzed for genetic relatedness. Only the first available sequence per participant was included. Inferred transmission networks ("clusters") were defined as ?2 sequences with ?1.5% genetic distance. Clusters including ?3 patients ("networks") were evaluated for clinical and demographic associations.ResultsOf 3697 sequences, 24% fell into inferred clusters: 155 clusters of 2 individuals ("dyads"), 54 clusters that included 3-14 individuals ("networks"), and 1 large cluster that included 336 individuals across all study sites. In multivariable analyses, factors associated with being in a cluster included not using antiretroviral (ARV) drugs at time of sampling (P < .001), sequence collected after 2004 (P < .001), CD4 cell count >350 cells/mL (P < .01), and viral load 10,000-100,000 copies/mL (P < .001) or >100,000 copies/mL (P < .001). In networks, women were more likely to cluster with other women (P < .001), and African Americans with other African Americans (P < .001).ConclusionsMolecular epidemiology can be applied to study HIV transmission networks in geographically and demographically diverse cohorts. Clustering was associated with lack of ARV use and higher viral load, implying transmission may be interrupted by earlier diagnosis and treatment. Observed female and African American networks reinforce the importance of diagnosis and prevention efforts targeted by sex and race.
| S-EPMC3529609 | biostudies-literature
Project description:BACKGROUND:Norovirus outbreaks in hospital settings are a common challenge for infection prevention teams. Given the high burden of norovirus in most communities, it can be difficult to distinguish between ongoing in-hospital transmission of the virus and new introductions from the community, and it is challenging to understand the long-term impacts of outbreak-associated viruses within medical systems using traditional epidemiological approaches alone. METHODS:Real-time metagenomic sequencing during an ongoing norovirus outbreak associated with a retrospective cohort study. RESULTS:We describe a hospital-associated norovirus outbreak that affected 13 patients over a 27-day period in a large, tertiary, pediatric hospital. The outbreak was chronologically associated with a spike in self-reported gastrointestinal symptoms among staff. Real-time metagenomic next-generation sequencing (mNGS) of norovirus genomes demonstrated that 10 chronologically overlapping, hospital-acquired norovirus cases were partitioned into 3 discrete transmission clusters. Sequencing data also revealed close genetic relationships between some hospital-acquired and some community-acquired cases. Finally, this data was used to demonstrate chronic viral shedding by an immunocompromised, hospital-acquired case patient. An analysis of serial samples from this patient provided novel insights into the evolution of norovirus within an immunocompromised host. CONCLUSIONS:This study documents one of the first applications of real-time mNGS during a hospital-associated viral outbreak. Given its demonstrated ability to detect transmission patterns within outbreaks and elucidate the long-term impacts of outbreak-associated viral strains on patients and medical systems, mNGS constitutes a powerful resource to help infection control teams understand, prevent, and respond to viral outbreaks.
| S-EPMC6735836 | biostudies-other
Project description:Control of norovirus outbreaks relies on enhanced hygiene measures, such as handwashing, surface cleaning, using disposable paper towels, and using separate toilets for sick and well persons. However, little is known about their effectiveness in limiting further spread of norovirus infections. We analyzed norovirus outbreaks in 7 camps at an international scouting jamboree in the Netherlands during 2004. Implementation of hygiene measures coincided with an 84.8% (95% predictive interval 81.2%-86.6%) reduction in reproduction number. This reduction was unexpectedly large but still below the reduction needed to contain a norovirus outbreak. Even more stringent control measures are required to break the chain of transmission of norovirus.
| S-EPMC2660689 | biostudies-literature
Project description:We report an increase in the proportion of genotype GI.6 norovirus outbreaks in the United States from 1.4% in 2010 to 7.7% in 2012 (p<0.001). Compared with non-GI.6 outbreaks, GI.6 outbreaks were characterized by summer seasonality, foodborne transmission, and non-health care settings.
| S-EPMC3739519 | biostudies-literature
Project description:To determine whether the norovirus strain GII.17 recently detected in Maryland, USA, (Hu/GII.17/Gaithersburg/2014/US) is spreading globally, we characterized the genome. High similarity with the norovirus GII.17 that caused recent outbreaks in Asia indicates that the same strain was present in the United States during the 2014-15 norovirus season (winter).
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Project description:In October 2009, a novel GII.12 norovirus strain emerged in the United States and caused 16% of all reported norovirus outbreaks during the winter season. Sequence analysis demonstrated a recombinant virus with a P2 region that was largely conserved compared with previously sequenced GII.12 strains.
| S-EPMC3381559 | biostudies-literature
Project description:CaliciNet, the outbreak surveillance network for noroviruses in the United States, was launched in March 2009. As of January 2011, twenty state and local health laboratories had been certified to submit norovirus sequences and epidemiologic outbreak data to CaliciNet. During the network's first year, 552 outbreaks were submitted to CaliciNet, of which 78 (14%) were associated with foodborne transmission. A total of 395 (72%) outbreaks were typed as GII.4, of which 298 (75%) belonged to a new variant, GII.4 New Orleans, which first emerged in October 2009. Analysis of the complete capsid and P2 region sequences confirmed that GII.4 New Orleans is distinct from previous GII.4 variants, including GII.4 Minerva (2006b).
| S-EPMC3381557 | biostudies-literature
Project description:In January 2015, an outbreak of undiagnosed human immunodeficiency virus (HIV) infections among persons who inject drugs (PWID) was recognized in rural Indiana. By September 2016, 205 persons in this community of approximately 4400 had received a diagnosis of HIV infection. We report results of new approaches to analyzing epidemiologic and laboratory data to understand transmission during this outbreak. HIV genetic distances were calculated using the polymerase region. Networks were generated using data about reported high-risk contacts, viral genetic similarity, and their most parsimonious combinations. Sample collection dates and recency assay results were used to infer dates of infection. Epidemiologic and laboratory data each generated large and dense networks. Integration of these data revealed subgroups with epidemiologic and genetic commonalities, one of which appeared to contain the earliest infections. Predicted infection dates suggest that transmission began in 2011, underwent explosive growth in mid-2014, and slowed after the declaration of a public health emergency. Results from this phylodynamic analysis suggest that the majority of infections had likely already occurred when the investigation began and that early transmission may have been associated with sexual activity and injection drug use. Early and sustained efforts are needed to detect infections and prevent or interrupt rapid transmission within networks of uninfected PWID.
| S-EPMC5853229 | biostudies-literature
Project description:The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been mutating since it was first sequenced in early January 2020. The genetic variants have developed into a few distinct clusters with different properties. Since the United States (US) has the highest number of viral infected patients globally, it is essential to understand the US SARS-CoV-2. Using genotyping, sequence-alignment, time-evolution, k-means clustering, protein-folding stability, algebraic topology, and network theory, we reveal that the US SARS-CoV-2 has four substrains and five top US SARS-CoV-2 mutations were first detected in China (2 cases), Singapore (2 cases), and the United Kingdom (1 case). The next three top US SARS-CoV-2 mutations were first detected in the US. These eight top mutations belong to two disconnected groups. The first group consisting of 5 concurrent mutations is prevailing, while the other group with three concurrent mutations gradually fades out. We identify that one of the top mutations, 27964C>T-(S24L) on ORF8, has an unusually strong gender dependence. Based on the analysis of all mutations on the spike protein, we further uncover that three of four US SASR-CoV-2 substrains become more infectious. Our study calls for effective viral control and containing strategies in the US.
| S-EPMC7430589 | biostudies-literature
Project description:Involvement of clinical pharmacists in the ICU attenuates costs, avoids adverse drug events, and reduces morbidity and mortality. This survey assessed services and activities of ICU pharmacists.DesignA 27-question, pretested survey.Setting1,220 U.S. institutions.SubjectsCritical care pharmacists.InterventionsElectronic questionnaire of pharmacy services and activities across clinical practice, education, scholarship, and administration.Measurements and main resultsA total of 401 (response rate of 35.4%) surveys representing 493 ICUs were completed. Median daily ICU census was 12 (interquartile range, 6-20) beds with 1 (interquartile range, 1-1.5) pharmacist full-time equivalent per ICU. Direct clinical ICU pharmacy services were available in 70.8% of ICUs. Pharmacists attended rounds 5 days (interquartile range, 4-5 d) per week with a median patient-to-pharmacist ratio of 17 (interquartile range, 12-26). The typical workweek consisted of 50% (interquartile range, 40-60%) direct ICU patient care, 10% (interquartile range, 8-16%) teaching, 8% (interquartile range, 5-18%) order processing, 5% (interquartile range, 0-20%) direct non-ICU patient care, 5% (interquartile range, 2-10%) administration, 5% (interquartile range, 0-10%) scholarship, and 0% (interquartile range, 0-5%) drug distribution. Common clinical activities as a percentage of the workweek were reviewing drug histories (28.5%); assessing adverse events (27.6%); and evaluating (26.1%), monitoring (23.8%), and managing (21.4%) drug therapies. Services were less likely to occur overnight or on weekends. Telemedicine was rarely employed. Dependent prescriptive authority (per protocol or via practice agreements) was available to 51.1% of pharmacists and independent prescriptive authority was provided by 13.4% of pharmacists. Educational services most frequently provided were inservices (97.6%) and experiential training of students or residents (89%). Education of ICU healthcare members was provided at a median of 5 times/mo (interquartile range, 3-15 times/mo). Most respondents were involved with ICU or departmental policies/guidelines (84-86.8%) and 65.7% conducted some form of scholarship.ConclusionsICU pharmacists have diverse and versatile responsibilities and provide several key clinical and nonclinical services. Initiatives to increase the availability of services are warranted.
| S-EPMC7803868 | biostudies-literature