A Framework for Detecting and Classifying Outbreaks of Gastrointestinal Disease

Outbreaks of gastrointestinal disease occur with some frequency in North America, resulting in considerably morbidity, mortality, and cost. Outbreak detection can be improved by using simulated outbreak data to build, validate, and evaluate models that aim to improve accuracy and timeliness of outbreak detection. We have constructed a microsimulation model that depicts reasonable outbreak scenarios in space and time, and explore the use of a hidden Markov model along with supervised learning algorithms to find unique space-time outbreak signatures useful for outbreak classification

A Framework for Detecting and Classifying Outbreaks of Gastrointestinal Disease

OBJECTIVE: To develop a methodological framework for detecting and classifying outbreaks of gastrointestinal disease on the island of Montreal, with the goal of improving early outbreak detection using simulated surveillance data. INTRODUCTION: Outbreaks of waterborne gastrointestinal disease occur routinely in North America, resulting in considerable morbidity, mortality, and cost (Hrudey, Payment et al. 2003). Outbreak detection methods generally attempt to identify anomalies in time, but do not identify the type or source of an outbreak. We seek to develop a framework for both detection and classification of outbreaks using information in both space and time. Outbreak detection can be improved by using simulated outbreak data to build, validate, and evaluate models that aim to improve accuracy and timeliness of outbreak detection. METHODS: To generate outbreak data, we used a previously validated microsimulation model depicting waterborne outbreaks of gastrointestinal disease (Okhmatovskaia et al. 2010). The model is parameterized based on outbreak characteristics such as concentration and duration of contamination, and calibrated to produce realistic outbreak data (e.g., emergency department visits from GI-illness, laboratory reporting to public health) in space and time. We are interested in identifying unique space-time signatures in the data that would allow not only detection, but also classification based on outbreak type. For example, to be able to detect and classify an outbreak as due to a water plant failure versus an food-borne illness based on unique space-time patterns, even though symptoms and temporal outbreak patterns may be similar. For the detection step, we use a hidden Markov model (HMM) that accounts for spatial information through a spatially correlated random effect with an exponential decay. HMMs have been used previously in disease mapping (Green 2002) but not widely in space-time disease outbreak detection. For the classification step, we use a supervised clustering algorithm to classify the outbreak by source (e.g., water plant location) and type (e.g., disease). RESULTS: Preliminary results for the detection step show that the HMM can distinguish accurately between regions in an outbreak state versus those in a normal state at each time period. Ongoing work for the detection step includes further evaluation of the HMM accuracy as a function of outbreak characteristics. For the classification step, we are evaluating the suitability of different supervised clustering algorithms for identifying the type of outbreak from the HMM results. CONCLUSIONS: If outbreaks are detected rapidly, interventions, such as boil-water advisories, are available to quickly and effectively limit the human and economic impacts. Traditional public health surveillance systems, however, frequently fail to detect waterborne disease outbreaks. Every disease outbreak has unique characteristics; simulation is the best method to estimate the capacity of syndromic surveillance to more efficiently detect different types of enteric disease outbreaks based on a variety of parameters. Outbreak detection can be improved with advances in data availability, such as syndromic surveillance data that will increase timeliness of detection, and space-time information to allow for simultaneous detection and classification of outbreaks by important characteristics (type of outbreak, source of outbreak)

Severity of Omicron (B.1.1.529) and Delta (B.1.617.2) SARS-CoV-2 infection among hospitalised adults: A prospective cohort study in Bristol, United KingdomResearch in context

Summary: Background: There is an urgent public health need to evaluate disease severity in adults hospitalised with Delta and Omicron SARS-CoV-2 variant infections. However, limited data exist assessing severity of disease in adults hospitalised with Omicron SARS-CoV-2 infections, and to what extent patient-factors, including vaccination, age, frailty and pre-existing disease, affect variant-dependent disease severity. Methods: A prospective cohort study of adults (≥18 years of age) hospitalised with acute lower respiratory tract disease at acute care hospitals in Bristol, UK conducted over 10-months. Delta or Omicron SARS-CoV-2 infection was defined by positive SARS-CoV-2 PCR and variant identification or inferred by dominant circulating variant. We constructed adjusted regression analyses to assess disease severity using three different measures: FiO2 >28% (fraction inspired oxygen), World Health Organization (WHO) outcome score >5 (assessing need for ventilatory support), and hospital length of stay (LOS) >3 days following admission for Omicron or Delta infection. Findings: Independent of other variables, including vaccination, Omicron variant infection in hospitalised adults was associated with lower severity than Delta. Risk reductions were 58%, 67%, and 16% for supplementary oxygen with >28% FiO2 [Relative Risk (RR) = 0.42 (95%CI: 0.34–0.52), P 5 [RR = 0.33 (95%CI: 0.21–0.50), P  3 days [RR = 0.84 (95%CI: 0.76–0.92), P < 0.001]. Younger age and vaccination with two or three doses were also independently associated with lower COVID-19 severity. Interpretation: We provide reassuring evidence that Omicron infection results in less serious adverse outcomes than Delta in hospitalised patients. Despite lower severity relative to Delta, Omicron infection still resulted in substantial patient and public health burden and an increased admission rate of older patients with Omicron which counteracts some of the benefit arising from less severe disease. Funding: AvonCAP is an investigator-led project funded under a collaborative agreement by Pfizer

2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.

In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV