Duration of viable virus shedding and polymerase chain reaction positivity of the SARS-CoV-2 Omicron variant in the upper respiratory tract: a systematic review and meta-analysis

Wu, Yu; Guo, Zirui; Yuan, Jie; Cao, Guiying; Wang, Yaping; Gao, Peng; Liu, Jue; M, Liu

doi:10.1016/j.ijid.2023.02.011

Cited by 12 publications

(9 citation statements)

References 34 publications

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“…In contrast, early viral variants required a longer time to be cleared from the upper respiratory tract. [26][27][28] In this study, the median duration of negative conversion duration was 7 days for both asymptomatic and mild symptomatic patients, which might indicate that asymptomatic and mild symptomatic patients carry the virus and are infectious for a similar duration of time. It was also worth noting that the symptomatic patients had significantly lower C t values than the asymptomatic patients in the study.…”

Section: Discussionmentioning

confidence: 59%

“…Our results found that 225 (40.8%) patients achieved a virus‐free status within 7 days (data not shown). In contrast, early viral variants required a longer time to be cleared from the upper respiratory tract 26–28 . In this study, the median duration of negative conversion duration was 7 days for both asymptomatic and mild symptomatic patients, which might indicate that asymptomatic and mild symptomatic patients carry the virus and are infectious for a similar duration of time.…”

Section: Discussionmentioning

confidence: 60%

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Clinical and virological features of asymptomatic and mild symptomatic patients with SARS‐CoV‐2 Omicron infection at Shanghai Fangcang shelter hospital

Zhang,

Kang,

Wang

et al. 2023

Immunity Inflam & Disease

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ObjectiveThe objective of this study is to evaluate and compare clinical and virological characteristics of asymptomatic and mild symptomatic patients of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) Omicron BA.2.2 variant infection and identify risk factors associated with the prolonged viral negative conversion duration.MethodsWe conducted a retrospective observational study in a Shanghai (China) Fangcang shelter hospital from April 9 to May 17, 2022. The patient‐related demographic or clinical data were retrospectively recorded. Comparisons of demographic and clinical characteristics between asymptomatic and mild‐symptomatic patients were performed. Cox regression was performed to identify the risk factors of prolonged viral negative conversion duration.ResultsA total of 551 patients confirmed with SARS‐CoV‐2 Omicron variant infection were enrolled in the study. Of these, 297 patients (53.9%) were asymptomatic and 254 patients (46.1%) had mild symptoms. When comparing the clinical and virological characteristics between the asymptomatic and mild symptomatic groups, several clinical parameters, including age, gender, time to viral clearance from the first positive swab, chronic comorbidities, and vaccination dose did not show statistically significant differences. In mild symptomatic patients, the median viral negative conversion duration (NCD) was 7 days (interquartile range [IQR]: 5–9), which was comparable to the median of 7 days (IQR: 5–10) in asymptomatic patients (p = .943). Multivariate Cox analysis revealed that patients age ≥ 60 years had a significantly higher hazard ratio (HR) for prolonged viral NCD (HR: 1.313; 95% confidence interval: 1.014–1.701, p = .039).ConclusionAsymptomatic and symptomatic patients with non‐severe SARS‐CoV‐2 Omicron BA.2.2 variant infection have similar clinical features and virological courses. Old age was an independent risk factor for prolonged SARS‐CoV‐2 conversion time.

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Section: Discussionmentioning

confidence: 59%

Section: Discussionmentioning

confidence: 60%

Clinical and virological features of asymptomatic and mild symptomatic patients with SARS‐CoV‐2 Omicron infection at Shanghai Fangcang shelter hospital

Zhang,

Kang,

Wang

et al. 2023

Immunity Inflam & Disease

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“…Yet our point estimates of the proportion remaining infectious after ten days (computed as α 10 ) would be 54.4 percent from the combined-variant data and 36.0 percent from the Omicron-only data. A meta-analysis of 29 clinical studies suggested that while the mean duration of polymerase chain reaction (PCR) positivity was 10.82 days, the mean duration of viral shedding was only 5.16 days [93]. Yet our point estimates of the mean duration of infectivity (computed as 1/(1 − α )) were 16.8 days from the combined-variant data and 10.3 days from the Omicron-only data.…”

Section: Discussionmentioning

confidence: 86%

Tight Fit of the SIR Dynamic Epidemic Model to Daily Cases of COVID-19 Reported During the 2021-2022 Omicron Surge in New York City: A Novel Approach

Harris

2023

Preprint

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We describe a novel approach to recovering the underlying parameters of the SIR dynamic epidemic model from observed data on case incidence or deaths. We formulate a discrete-time approximation to the original continuous-time model and search for the parameter vector that minimizes the standard least squares criterion function. We show that the gradient vector and matrix of second-order derivatives of the criterion function with respect to the parameters adhere to their own systems of difference equations and thus can be exactly calculated iteratively. Applying our new approach, we estimate four-parameter SIR models on two types of datasets: (1) daily reported cases of COVID-19 during the SARS-CoV-2 Omicron/BA.1 surges of December 2021 - March 2022 in New York City and Los Angeles County; and (2) weekly deaths from a plague outbreak on the Isle of Bombay during December 1905 - July 1906, originally studied by Kermack and McKendrick in their now-classic 1927 paper. The estimated parameters from the COVID-19 data suggest a duration of persistent infectivity beyond that reported in small-scale clinical studies of mostly symptomatic subjects. The estimated parameters from the plague data suggest that the Bombay outbreak was in fact driven by pulmonic rather than bubonic plague.

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“…To assess the accuracy of our outbreak reconstruction model relative to existing ones, we first generated a dataset of 100 synthetic outbreaks. We modeled the generation intervals, latent period durations, and infectious period durations as a stochastic-epidemic process, with each time interval independently sampled from a pre-specified probability distribution based on existing studies of SARS-CoV-2 Omicron variant transmission [33,34] (see Figure 3A and Methods ). We simulated transmission networks by generating random trees in which the number of offspring of each case follows a negative binomial distribution with a basic reproductive number ( R 0 ) of 2.5 and overdispersion parameter ( k ) of 0.1 [35], and extracting a random subtree of 10–15 individuals to be our cluster, discarding trees in which no such subcluster existed.…”

Section: Resultsmentioning

confidence: 99%

Inferring Viral Transmission Pathways from Within-Host Variation

Specht,

Petros,

Moreno

et al. 2023

Preprint

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Genome sequencing can offer critical insight into pathogen spread in viral outbreaks, but existing transmission inference methods use simplistic evolutionary models and only incorporate a portion of available genetic data. Here, we develop a robust evolutionary model for transmission reconstruction that tracks the genetic composition of within-host viral populations over time and the lineages transmitted between hosts. We confirm that our model reliably describes within-host variant frequencies in a dataset of 134,682 SARS-CoV-2 deep-sequenced genomes from Massachusetts, USA. We then demonstrate that our reconstruction approach infers transmissions more accurately than two leading methods on synthetic data, as well as in a controlled outbreak of bovine respiratory syncytial virus and an epidemiologically-investigated SARS-CoV-2 outbreak in South Africa. Finally, we apply our transmission reconstruction tool to 5,692 outbreaks among the 134,682 Massachusetts genomes. Our methods and results demonstrate the utility of within-host variation for transmission inference of SARS-CoV-2 and other pathogens, and provide an adaptable mathematical framework for tracking within-host evolution.

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Duration of viable virus shedding and polymerase chain reaction positivity of the SARS-CoV-2 Omicron variant in the upper respiratory tract: a systematic review and meta-analysis

Cited by 12 publications

References 34 publications

Clinical and virological features of asymptomatic and mild symptomatic patients with SARS‐CoV‐2 Omicron infection at Shanghai Fangcang shelter hospital

Clinical and virological features of asymptomatic and mild symptomatic patients with SARS‐CoV‐2 Omicron infection at Shanghai Fangcang shelter hospital

Tight Fit of the SIR Dynamic Epidemic Model to Daily Cases of COVID-19 Reported During the 2021-2022 Omicron Surge in New York City: A Novel Approach

Inferring Viral Transmission Pathways from Within-Host Variation

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