Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data

Zhao, Shi; Tang, Biao; Musa, Salihu S.; Ma, Shujuan; Zhang, Jiayue; Zeng, Minyan; Yun, Qingping; Guo, Wei; Zheng, Yixiang; Yang, Zu‐Yao; Peng, Zhihang; Chong, Ka Chun; Javanbakht, Mohammad; He, Daihai; Wang, Maggie Haitian

doi:10.1016/j.epidem.2021.100482

Cited by 64 publications

(60 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“… 50 – 53 To set up the analysis for COVID-19, we consider w as a Gamma distribution having mean (±SD) values of 5.3 (±2.1) days by averaging the GT estimates from the existing literatures. 50 – 57 Slight variation in the settings of the GT will not affect our main findings.…”

Section: Methodsmentioning

confidence: 82%

Exploring the Interaction between E484K and N501Y Substitutions of SARS-CoV-2 in Shaping the Transmission Advantage of COVID-19 in Brazil: A Modeling Study

Zhao

Ran

Han

2021

The American Journal of Tropical Medicine and Hygiene

Self Cite

View full text Add to dashboard Cite

The COVID-19 pandemic poses serious threats to global health, and the emerging mutation in SARS-CoV-2 genomes is one of the major challenges of disease control. Considering the growth of epidemic curve and the circulating SARS-CoV-2 variants in Brazil, the role of locally prevalent E484K and N501Y substitutions in contributing to the epidemiological outcomes is of public health interest for investigation. We developed a likelihood-based statistical framework to reconstruct reproduction numbers, estimate transmission advantage associated with different SARS-CoV-2 variants regarding the marking (identifying) 484K and 501Y substitutions (including Alpha, Zeta, and Gamma variants) in Brazil, and explored the interactive effects of genetic activities on transmission advantage marked by these two mutations. We found a significant transmission advantage associated with the 484K/501Y variants (including P.1 or Gamma variants), which increased the infectivity significantly by 23%. In contrast and by comparison to Gamma variants, E484K or N501Y (including Alpha or Zeta variants) substitution alone appeared less likely to secure a concrete transmission advantage in Brazil. Our finding indicates that the combined impact of genetic activities on transmission advantage marked by 484K/501Y outperforms their independent contributions in Brazil, which implies an interactive effect in shaping the increase in the infectivity of COVID-19. Future studies are needed to investigate the mechanisms of how E484K and N501Y mutations and the complex genetic mutation activities marked by them in SARS-CoV-2 affect the transmissibility of COVID-19.

show abstract

Section: Methodsmentioning

confidence: 82%

Exploring the Interaction between E484K and N501Y Substitutions of SARS-CoV-2 in Shaping the Transmission Advantage of COVID-19 in Brazil: A Modeling Study

Zhao

Ran

Han

2021

The American Journal of Tropical Medicine and Hygiene

Self Cite

View full text Add to dashboard Cite

show abstract

“…The generative time has been estimated through the synchronization between the signals in the calibration steps. This is equivalent to the delay estimate used by RtLive and Epiforecast and other reconstruction infection estimates as 17 , 18 , 47 , 48 as in Fig. 3 .…”

Section: Methodsmentioning

confidence: 96%

On the use of aggregated human mobility data to estimate the reproduction number

Vanni

Lambert

Palatella³

et al. 2021

Sci Rep

View full text Add to dashboard Cite

The reproduction number of an infectious disease, such as CoViD-19, can be described through a modified version of the susceptible-infected-recovered (SIR) model with time-dependent contact rate, where mobility data are used as proxy of average movement trends and interpersonal distances. We introduce a theoretical framework to explain and predict changes in the reproduction number of SARS-CoV-2 in terms of aggregated individual mobility and interpersonal proximity (alongside other epidemiological and environmental variables) during and after the lockdown period. We use an infection-age structured model described by a renewal equation. The model predicts the evolution of the reproduction number up to a week ahead of well-established estimates used in the literature. We show how lockdown policies, via reduction of proximity and mobility, reduce the impact of CoViD-19 and mitigate the risk of disease resurgence. We validate our theoretical framework using data from Google, Voxel51, Unacast, The CoViD-19 Mobility Data Network, and Analisi Distribuzione Aiuti.

show abstract

“…The rate at which contacts occur is determined by the mixing patterns of each age group. The latent period and average generation time were set to be 4.4 [ 28 – 30 ] and 7 [ 31 ] days, respectively. We consider a basic reproductive number ( R 0 ) of 6.0 according to estimates for the SARS-CoV-2 Delta variant [ 1 – 4 , 6 – 12 , 16 – 18 ].…”

Section: Methodsmentioning

confidence: 99%

Investigating vaccine-induced immunity and its effect in mitigating SARS-CoV-2 epidemics in China

Liu

Zhang

Cai

et al. 2022

BMC Med

View full text Add to dashboard Cite

Background To allow a return to a pre-COVID-19 lifestyle, virtually every country has initiated a vaccination program to mitigate severe disease burden and control transmission. However, it remains to be seen whether herd immunity will be within reach of these programs. Methods We developed a compartmental model of SARS-CoV-2 transmission for China, a population with low prior immunity from natural infection. Two vaccination programs were tested and model-based estimates of the immunity level in the population were provided. Results We found that it is unlikely to reach herd immunity for the Delta variant given the relatively low efficacy of the vaccines used in China throughout 2021 and the lack of prior natural immunity. We estimated that, assuming a vaccine efficacy of 90% against the infection, vaccine-induced herd immunity would require a coverage of 93% or higher of the Chinese population. However, even when vaccine-induced herd immunity is not reached, we estimated that vaccination programs can reduce SARS-CoV-2 infections by 50–62% in case of an all-or-nothing vaccine model and an epidemic starts to unfold on December 1, 2021. Conclusions Efforts should be taken to increase population’s confidence and willingness to be vaccinated and to develop highly efficacious vaccines for a wide age range.

show abstract

Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data

Cited by 64 publications

References 60 publications

Exploring the Interaction between E484K and N501Y Substitutions of SARS-CoV-2 in Shaping the Transmission Advantage of COVID-19 in Brazil: A Modeling Study

Exploring the Interaction between E484K and N501Y Substitutions of SARS-CoV-2 in Shaping the Transmission Advantage of COVID-19 in Brazil: A Modeling Study

On the use of aggregated human mobility data to estimate the reproduction number

Investigating vaccine-induced immunity and its effect in mitigating SARS-CoV-2 epidemics in China

Contact Info

Product

Resources

About