Journal article
Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19
JE Stockdale, K Susvitasari, P Tupper, B Sobkowiak, N Mulberry, A Gonçalves da Silva, AE Watt, NL Sherry, C Minko, BP Howden, CR Lane, C Colijn
Nature Communications | NATURE PORTFOLIO | Published : 2023
Abstract
Serial intervals – the time between symptom onset in infector and infectee – are a fundamental quantity in infectious disease control. However, their estimation requires knowledge of individuals’ exposures, typically obtained through resource-intensive contact tracing efforts. We introduce an alternate framework using virus sequences to inform who infected whom and thereby estimate serial intervals. We apply our technique to SARS-CoV-2 sequences from case clusters in the first two COVID-19 waves in Victoria, Australia. We find that our approach offers high resolution, cluster-specific serial interval estimates that are comparable with those obtained from contact data, despite requiring no kn..
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Grants
Awarded by State Government of Victoria
Funding Acknowledgements
& nbsp;With this work, we would like to remember Anders Goncalves da Silva, who sadly passed away during the late stage of this project, for his thoughtful contributions and for bringing our team together. We thank the public health, clinical and microbiology staff across Victoria who have been involved in the testing, clinical care and public health responses to COVID-19. We gratefully acknowledge the originating and submitting laboratories of sequences deposited in the GISAID Database that were used in this study. References to these laboratories are available in Supplementary Data & nbsp;1. Figure & nbsp;1 was created with BioRender.com. This work was funded by the Victorian Government (A.G.d.S., C.M., N.L.S. and C.R.L.), who also funded the sequencing costs. Funding was also received from the National Health and Medical Research Council (NHMRC) Australia, through the Medical Research Future Fund: Coronavirus Research Response: 2020 Tracking COVID-19 in Australia using Genomics Grant Opportunity MRF9200006 (B.P.H. and A.E.W.) and NHMRC partnership grant: An evidence-based framework for establishing public health microbial genomics in Australia APP1149991 (B.P.H. and A.G.d.S.). The authors received funding from Natural Science and Engineering Research Council (Canada) Discovery Grants RGPIN-2019-06911 (P.T.), RGPIN-2019-06624 (C.C.), Michael Smith Health Research BC COV-2020-1010 (C.C.) and the Federal Government of Canada's Canada 150 Research Chair programme (C.C.). B.P.H. is supported by an NHMRC Investigator Grant GNT1196103.