Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Nature, Journal Year: 2022, Volume and Issue: 603(7902), P. 679 - 686

Published: Jan. 7, 2022

Abstract The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. first was associated with a mix of lineages, while the second and third waves were driven Beta (B.1.351) Delta (B.1.617.2) variants, respectively 1–3 . In November 2021, genomic surveillance teams South Botswana detected new variant rapid resurgence infections Gauteng province, Africa. Within days genome being uploaded, it designated concern (Omicron, B.1.1.529) World Health Organization and, within weeks, had identified 87 countries. Omicron is exceptional for carrying over 30 mutations spike glycoprotein, which are predicted to influence antibody neutralization function 4 Here we describe profile early transmission dynamics Omicron, highlighting spread regions high levels population immunity.

Language: Английский

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Practical considerations for measuring the effective reproductive number, Rt

PLoS Computational Biology, Journal Year: 2020, Volume and Issue: 16(12), P. e1008409 - e1008409

Published: Dec. 10, 2020

Estimation of the effective reproductive number Rt is important for detecting changes in disease transmission over time. During Coronavirus Disease 2019 (COVID-19) pandemic, policy makers and public health officials are using to assess effectiveness interventions inform policy. However, estimation from available data presents several challenges, with critical implications interpretation course pandemic. The purpose this document summarize these illustrate them examples synthetic data, and, where possible, make recommendations. For near real-time Rt, we recommend approach Cori colleagues, which uses before time t empirical estimates distribution between infections. Methods that require after t, such as Wallinga Teunis, conceptually methodologically less suited estimation, but may be appropriate retrospective analyses how individuals infected at different points contributed spread. We advise caution when methods derived Bettencourt Ribeiro, resulting biased if underlying structural assumptions not met. Two key challenges common all approaches accurate specification generation interval reconstruction series new infections observations occurring long moment transmission. Naive dealing observation delays, subtracting delays sampled a distribution, can introduce bias. provide suggestions mitigate other technical highlight open problems estimation.

Language: Английский

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Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2

Environmental Health Perspectives, Journal Year: 2022, Volume and Issue: 130(5)

Published: May 1, 2022

Background: The effective reproductive number, Re, is a critical indicator to monitor disease dynamics, inform regional and national policies, estimate the effectiveness of interventions. It describes average number new infections caused by single infectious person through time. To date, Re estimates are based on clinical data such as observed cases, hospitalizations, and/or deaths. These temporarily biased when testing or reporting strategies change. Objectives: We show that dynamics severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater can be used near real time, independent without associated biases. Methods: collected longitudinal measurements SARS-CoV-2 Zurich, Switzerland, San Jose, California, USA. combined this with information temporal shedding (the load distribution) time series proportional daily COVID-19 infection incidence. estimated wastewater-based from Results: method worked robustly two different countries matrices. resulting were similar case report deaths among each other. further provide details effect sampling frequency distribution ability infer Re. Discussion: our knowledge, first has been wastewater. This provides low-cost, rapid, way monitoring during ongoing pandemic applicable future epidemiology targeting other pathogens. https://doi.org/10.1289/EHP10050

Language: Английский

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Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high

Water Research, Journal Year: 2021, Volume and Issue: 200, P. 117252 - 117252

Published: May 17, 2021

Wastewater-based epidemiology (WBE) has been shown to coincide with, or anticipate, confirmed COVID-19 case numbers. During periods with high test positivity rates, however, numbers may be underreported, whereas wastewater does not suffer from this limitation. Here we investigated how the dynamics of new infections estimated based on monitoring cases compare true incidence dynamics. We focused first pandemic wave in Switzerland (February April, 2020), when ranged up 26%. SARS-CoV-2 RNA loads were determined 2–4 times per week three Swiss treatment plants (Lugano, Lausanne and Zurich). Wastewater data combined a shedding load distribution an infection-to-case confirmation delay distribution, respectively, estimate infection Finally, estimates compared reference by validated compartmental model. Incidence found better track timing shape peak cases. In contrast, confirmations provided subsequent decline infections. Under regime high-test WBE thus provides critical information that is complementary clinical monitor trajectory.

Language: Английский

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Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 16, 2024

Abstract Many studies have used mobile device location data to model SARS-CoV-2 dynamics, yet relationships between mobility behavior and endemic respiratory pathogens are less understood. We studied the effects of population on transmission 17 viruses in Seattle over a 4-year period, 2018-2022. Before 2020, visits schools daycares, within-city mixing, visitor inflow preceded or coincided with seasonal outbreaks viruses. Pathogen circulation dropped substantially after initiation COVID-19 stay-at-home orders March 2020. During this was positive, leading indicator all lagging negatively correlated activity. Mobility briefly predictive when restrictions relaxed but associations weakened subsequent waves. The rebound heterogeneously timed exhibited stronger, longer-lasting than SARS-CoV-2. Overall, is most virus during periods dramatic behavioral change at beginning epidemic

Language: Английский

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estimateR: an R package to estimate and monitor the effective reproductive number

BMC Bioinformatics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Aug. 11, 2023

Abstract Background Accurate estimation of the effective reproductive number ( $$R_e$$ Re ) epidemic outbreaks is central relevance to public health policy and decision making. We present estimateR, an R package for through time from delayed observations infection events. Such include confirmed cases, hospitalizations or deaths. The implements methodology Huisman et al. but modularizes procedure allow easy implementation new alternatives currently available methods. Users can tailor their analyses according particular use case by choosing among implemented options. Results estimateR allows users estimate outbreak based on observed hospitalization, death any other type event documenting past infections, in a fast timely fashion. validated with simulation study: yielded estimates comparable alternative publicly methods while being around two orders magnitude faster. then applied empirical case-confirmation incidence data COVID-19 nine countries dengue fever Brazil; parallel, already (i) SARS-CoV-2 measurements wastewater (ii) study influenza transmission clinical studies. In summary, this provides flexible various diseases datasets. Conclusions modular extendable tool designed surveillance retrospective investigation. It extends method developed makes it variety pathogens, scenarios, observation types. Estimates obtained be interpreted directly used inform more complex models (e.g. forecasting) value .

Language: Английский

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Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(2)

Published: Jan. 4, 2024

We estimate the basic reproductive number and case counts for 15 distinct Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks, distributed across 11 populations (10 countries one cruise ship), based solely on phylodynamic analyses of genomic data. Our results indicate that, prior to significant public health interventions, numbers 10 (out 15) these outbreaks are similar, with median posterior estimates ranging between 1.4 2.8. These provide a view which is complementary that provided by those traditional line listing The genomic-based arguably less susceptible biases resulting from differences in testing protocols, intensity, import cases into community interest. In reported here, data primarily information regarding samples belong particular outbreak. observe once identified, sampling dates carry majority number. Finally, we genome-based cumulative infections each For 7 out studied, confirmed much bigger than estimated sequence data, possible explanation being presence unsequenced populations.

Language: Английский

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Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland

Epidemics, Journal Year: 2021, Volume and Issue: 37, P. 100480 - 100480

Published: Aug. 9, 2021

In December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now named B.1.1.7. Based on initial data from UK and later other countries, this variant was estimated to have transmission fitness advantage around 40-80 % (Volz et al., 2021; Leung Davies 2021).

Language: Английский

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Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges

PLOS Digital Health, Journal Year: 2022, Volume and Issue: 1(6), P. e0000052 - e0000052

Published: June 27, 2022

The time-varying reproduction number (R t ) is an important measure of transmissibility during outbreaks. Estimating whether and how rapidly outbreak growing > 1) or declining < can inform the design, monitoring adjustment control measures in real-time. We use a popular R package for estimation, EpiEstim, as case study to evaluate contexts which estimation methods have been used identify unmet needs would enable broader applicability these A scoping review, complemented by small EpiEstim user survey, highlight issues with current approaches, including quality input incidence data, inability account geographical factors, other methodological issues. summarise software developed tackle problems identified, but conclude that significant gaps remain should be addressed easier, more robust applicable epidemics.

Language: Английский

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Do COVID-19 containment measures work? Evidence from Switzerland

Zeitschrift für schweizerische Statistik und Volkswirtschaft/Schweizerische Zeitschrift für Volkswirtschaft und Statistik/Swiss journal of economics and statistics, Journal Year: 2022, Volume and Issue: 158(1)

Published: Feb. 5, 2022

We study the interplay of non-pharmaceutical containment measures, human behavior, and spread COVID-19 in Switzerland. First, we collect sub-national data construct indices that capture stringency measures at cantonal level. Second, use a vector autoregressive model to analyze feedback effects between our variables interest via structural impulse responses. Our results suggest increases lead significant reduction weekly infections as well debit card transactions, which serve proxy for behavioral changes population. Furthermore, analyzing different policy individually shows business closures, recommendations work from home, restrictions on gatherings have been particularly effective containing Finally, findings indicate sizeable voluntary transactions response positive infection shock.

Language: Английский

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