High infectiousness immediately before COVID-19 symptom onset highlights the importance of continued contact tracing
- University of Oxford, United Kingdom
- University of Warwick, United Kingdom
Abstract
Background: Understanding changes in infectiousness during SARS-COV-2 infections is critical to assess the effectiveness of public health measures such as contact tracing.
Methods: Here, we develop a novel mechanistic approach to infer the infectiousness profile of SARS-COV-2 infected individuals using data from known infector-infectee pairs. We compare estimates of key epidemiological quantities generated using our mechanistic method with analogous estimates generated using previous approaches.
Results: The mechanistic method provides an improved fit to data from SARS-CoV-2 infector-infectee pairs compared to commonly used approaches. Our best-fitting model indicates a high proportion of presymptomatic transmissions, with many transmissions occurring shortly before the infector develops symptoms.
Conclusions: High infectiousness immediately prior to symptom onset highlights the importance of continued contact tracing until effective vaccines have been distributed widely, even if contacts from a short time window before symptom onset alone are traced.
Funding: Engineering and Physical Sciences Research Council (EPSRC).
Data availability
All data generated or analysed during this study are included in the manuscript and supporting files. A source data file has been provided for Figure 2, containing the SARS-CoV-2 transmission pair data used in our analyses. These data were originally reported in references (3,10,29-31), and the combined data were also considered in reference (4). Code for reproducing our results is available at https://github.com/will-s-hart/COVID-19-Infectiousness-Profile.
Article and author information
Author details
William Stephen Hart
Funding
Engineering and Physical Sciences Research Council (Excellence Award)
- William Stephen Hart
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Jennifer Flegg, The University of Melbourne, Australia
Version history
- Received: December 7, 2020
- Accepted: April 25, 2021
- Accepted Manuscript published: April 26, 2021 (version 1)
- Version of Record published: June 11, 2021 (version 2)
Copyright
© 2021, Hart et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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High infectiousness immediately before COVID-19 symptom onset highlights the importance of continued contact tracing
eLife 10:e65534.
https://doi.org/10.7554/eLife.65534
Further reading
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- Epidemiology and Global Health
- Medicine
- Microbiology and Infectious Disease
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- Epidemiology and Global Health
Background:
The Zanzibar archipelago of Tanzania has become a low-transmission area for Plasmodium falciparum. Despite being considered an area of pre-elimination for years, achieving elimination has been difficult, likely due to a combination of imported infections from mainland Tanzania and continued local transmission.
Methods:
To shed light on these sources of transmission, we applied highly multiplexed genotyping utilizing molecular inversion probes to characterize the genetic relatedness of 282 P. falciparum isolates collected across Zanzibar and in Bagamoyo district on the coastal mainland from 2016 to 2018.
Results:
Overall, parasite populations on the coastal mainland and Zanzibar archipelago remain highly related. However, parasite isolates from Zanzibar exhibit population microstructure due to the rapid decay of parasite relatedness over very short distances. This, along with highly related pairs within shehias, suggests ongoing low-level local transmission. We also identified highly related parasites across shehias that reflect human mobility on the main island of Unguja and identified a cluster of highly related parasites, suggestive of an outbreak, in the Micheweni district on Pemba island. Parasites in asymptomatic infections demonstrated higher complexity of infection than those in symptomatic infections, but have similar core genomes.
Conclusions:
Our data support importation as a main source of genetic diversity and contribution to the parasite population in Zanzibar, but they also show local outbreak clusters where targeted interventions are essential to block local transmission. These results highlight the need for preventive measures against imported malaria and enhanced control measures in areas that remain receptive to malaria reemergence due to susceptible hosts and competent vectors.
Funding:
This research was funded by the National Institutes of Health, grants R01AI121558, R01AI137395, R01AI155730, F30AI143172, and K24AI134990. Funding was also contributed from the Swedish Research Council, Erling-Persson Family Foundation, and the Yang Fund. RV acknowledges funding from the MRC Centre for Global Infectious Disease Analysis (reference MR/R015600/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 program supported by the European Union. RV also acknowledges funding by Community Jameel.
