Yannan Shen

2025-03-01

The Annals of Applied Statistics (publié)

arxiv.org

Development of a Framework for Establishing 'Gold Standard' Outbreak Data from Submitted SARS-CoV-2 Genome Samples

Russell Steele

Philip Abdelmalik

Submitted genomic data for respiratory viruses reflect the emergence and spread of new variants. Although delays in submission limit the uti… (voir plus)lity of these data for prospective surveillance, they may be useful for evaluating other surveillance sources. However, few studies have investigated the use of these data for evaluating aberration detection in surveillance systems. Our study used a Bayesian online change point detection algorithm (BOCP) to detect increases in the number of submitted genome samples as a means of establishing 'gold standard' dates of outbreak onset in multiple countries. We compared models using different data transformations and parameter values. BOCP detected change points that were not sensitive to different parameter settings. We also found data transformations were essential prior to change point detection. Our study presents a framework for using global genomic submission data to develop 'gold standard' dates about the onset of outbreaks due to new viral variants.

2024-08-22

Medical Informatics Europe (publié)

BAND: Biomedical Alert News Dataset

Zihao Fu

Meiru Zhang

Zaiqiao Meng

Anya Okhmatovskaia

Nigel Collier

2024-01-01

AAAI (publié)

arxiv.org

A three-state coupled Markov switching model for COVID-19 outbreaks across Quebec based on hospital admissions (preprint)

Dirk Douwes-Schultz

Alexandra M. Schmidt

2023-02-05

ArXiv (prépublication)

arxiv.org

BioCaster in 2021: automatic disease outbreaks detection from global news media

Zaiqiao Meng

Anya Okhmatovskaia

Maxime Polleri

Guido Powell

Zihao Fu

Iris Ganser

Meiru Zhang

Nicholas B King

Nigel Collier

2022-07-28

Bioinformatics (publié)

A Conceptual Framework for Representing Events Under Public Health Surveillance

Anya Okhmatovskaia

Iris Ganser

Nigel Collier

Nicholas B King

Zaiqiao Meng

Information integration across multiple event-based surveillance (EBS) systems has been shown to improve global disease surveillance in expe… (voir plus)rimental settings. In practice, however, integration does not occur due to the lack of a common conceptual framework for encoding data within EBS systems. We aim to address this gap by proposing a candidate conceptual framework for representing events and related concepts in the domain of public health surveillance.

2022-05-25

Medical Informatics Europe (publié)

Monitoring non-pharmaceutical public health interventions during the COVID-19 pandemic

Guido Powell

Iris Ganser

Qulu Zheng

Chris Grundy

Anya Okhmatovskaia

2021-08-24

Scientific Data (publié)

Global Surveillance of COVID-19 by mining news media using a multi-source dynamic embedded topic model

Yue Li

Pratheeksha Nair

Zhi Wen

Imane Chafi

Anya Okhmatovskaia

Guido Powell

2020-11-10

Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (publié)

Importation of SARS-CoV-2 following the "semaine de relache" and Quebec's (Canada) COVID-19 burden - a mathematical modeling study

Arnaud Godin

Yiqing Xia

Sharmistha Mishra

Dirk Douwes-Schultz

Maxime Lavigne

Mélanie Drolet

Alexandra M. Schmidt

Marc Brisson

Mathieu Maheu-Giroux

Background: The Canadian epidemics of COVID-19 exhibit distinct early trajectories, with Quebec bearing a very high initial burden. The sema… (voir plus)ine de relache, or March break, took place two weeks earlier in Quebec as compared to the rest of Canada. This event may have played a role in the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to examine the role of case importation in the early transmission dynamics of SARS-CoV-2 in Quebec. Methods: Using detailed surveillance data, we developed and calibrated a deterministic SEIR-type compartmental model of SARS-CoV-2 transmission. We explored the impact of altering the number of imported cases on hospitalizations. Specifically, we investigated scenarios without case importation after March break, and as scenarios where cases were imported with the same frequency/timing as neighboring Ontario. Results: A total of 1,544 and 1,150 returning travelers were laboratory-confirmed in Quebec and Ontario, respectively (with symptoms onset before 2020-03-25). The cumulative number of hospitalizations could have been reduced by 55% (95% credible interval [95%CrI]: 51-59%) had no cases been imported after Quebec's March break. However, had Quebec experienced Ontario's number of imported cases, cumulative hospitalizations would have only been reduced by 12% (95%CrI: 8-16%). Interpretation: Our results suggest that case importation played an important role in the early spread of COVID-19 in Quebec. Yet, heavy importation of SARS-CoV-2 in early March could be insufficient to resolve interprovincial heterogeneities in cumulative hospitalizations. The importance of other factors -public health preparedness, responses, and capacity- should be investigated.

2020-10-25

International Journal of Infectious Diseases (publié)

The role of case importation in explaining differences in early SARS-CoV-2 transmission dynamics in Canada—A mathematical modeling study of surveillance data

Arnaud Godin

Yiqing Xia

Sharmistha Mishra

Dirk Douwes-Schultz

Maxime Lavigne

Mélanie Drolet

Alexandra M. Schmidt

Marc Brisson

Mathieu Maheu-Giroux

2020-10-25

International Journal of Infectious Diseases (publié)