Making waves: Integrating wastewater surveillance with dynamic modeling to track and predict viral outbreaks

Phan, Tin; Brozak, Samantha; Pell, Bruce; Oghuan, Jeremiah; Gitter, Anna; Hu, T.; Ribeiro, Ruy M.; Ke, Ruian; Mena, Kristina D.; Perelson, Alan S.; Kuang, Yang; Wu, Fuqing

doi:10.1016/j.watres.2023.120372

Cited by 2 publications

(1 citation statement)

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“…In viral infections, the duration of viral shedding has been reported to be associated with infectivity and transmissibility and is a crucial factor in infection prevention and control [ 24 ]. Importantly, predicting viral shedding has important implications for communities, such as linking viral load data in sewage to the number of infected cases in the community to predict trends in clinically reported cases, which may be much higher than the number of reported cases [ 28 – 30 ]. As a result, it is vital to explore the viral shedding and its associated factors for individuals with Omicron variants [ 31 ].…”

Section: Discussionmentioning

confidence: 99%

A robust web-based tool to predict viral shedding in patients with Omicron SARS-CoV-2 variants

Zhang,

Gai,

Wang

et al. 2024

ERJ Open Res

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BackgroundData on viral kinetics and variants affecting the duration of viral shedding (VS) were limited. Our objective was to determine VS in distinct SARS-CoV-2 variants, including Omicron BA.4/5 and BF.7, and to identify the relevant influencing factors.MethodsWe carried out a longitudinal cohort study at Beijing Xiaotangshan Fangcang shelter hospital from May to June of 2022 (Omicron BA.4/5) and from November to December of 2022 (Omicron BF.7). Nucleocapsid protein (N) and open reading frame (ORF) genes were considered as the target genes of the reverse transcription-polymerase chain reaction. The daily results of cycle threshold (CT), including lowest ORF1ab-CT values for day1-day3 post of hospitalisation (CT3minORF) and lowest N-CT values for day1-day3 post of hospitalisation (CT3minN), and demographic and clinical characteristics were collected.ResultsA total of 1433 patients with COVID-19 were recruited from Fangcang shelter hospital, in which 278 patients were diagnosed with Omicron BA.4/5 and 1155 patients with Omicron BF.7. Patients with BF.7 infection showed a longer duration of VS. The duration of VS was associated with variants, age, alcohol use, the severity of COVID-19, and CT3minN. Moreover, the nomogram had excellent accuracy in predicting VS.ConclusionsOur results indicated that patients with Omicron BF.7 had a longer period of contagiousness than those with BA.4/5. The duration of VS was affected by a variety of factors and the nomogram may become an applicable clinical instrument to predict VS. Furthermore, we developed a new COVID-19 viral shedding predicting (CVSP) model that can accurately predict the duration of VS for COVID-19 and created a user-friendly website to easily apply this prediction model (https://puh3.shinyapps.io/CVSP_Model/).

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