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Data for Infection patterns of endemic human coronaviruses in rural households in coastal Kenya
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Nyaguthii, Dickson Machira, Otieno, Grieven P., Kombe, Ivy K., Koech, Dorothy C., Mutunga, Martin, Medley, Graham F., Nokes, D. James and Munywoki, Patrick K. (2021) Data for Infection patterns of endemic human coronaviruses in rural households in coastal Kenya. [Dataset]
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Official URL: https://doi.org/10.7910/DVN/CPJ9B4
Abstract
Background: The natural history and transmission patterns of endemic human coronaviruses are of increased interest following the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Methods: In rural Kenya 483 individuals from 47 households were followed for six months (2009-10) with nasopharyngeal swabs collected twice weekly regardless of symptoms. A total of 16,918 swabs were tested for human coronavirus (hCoV) OC43, NL63 and 229E and other respiratory viruses using polymerase chain reaction. Results: From 346 (71.6%) household members, 629 hCoV infection episodes were defined, with 36.3% being symptomatic: varying by hCoV type and decreasing with age. Symptomatic episodes (aHR=0.6 (95% CI:0.5-0.8) or those with elevated peak viral load (medium aHR=0.4 (0.3-0.6); high aHR=0.31 (0.2-0.4)) had longer viral shedding compared to their respective counterparts. Homologous reinfections were observed in 99 (19.9%) of 497 first infections. School-age children (55%) were the most common index cases with those having medium (aOR=5.3 (2.3 – 12.0)) or high (8.1 (2.9 - 22.5)) peak viral load most often generating secondary cases. Conclusion: Household coronavirus infection was common, frequently asymptomatic and mostly introduced by school-age children. Secondary transmission was influenced by viral load of index cases. Homologous-type reinfection was common. These data may be insightful for SARS-CoV-2.
Item Type: | Dataset | ||||||||||||
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Subjects: | Q Science > QR Microbiology | ||||||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||||||
Type of Data: | Observational data | ||||||||||||
Library of Congress Subject Headings (LCSH): | Coronaviruses -- Kenya, Coronaviruses -- Reproduction | ||||||||||||
Publisher: | University of Warwick, School of Life Sciences | ||||||||||||
Official Date: | 10 March 2021 | ||||||||||||
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Status: | Not Peer Reviewed | ||||||||||||
Publication Status: | Published | ||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||||||
Copyright Holders: | University of Warwick | ||||||||||||
Description: | Data record consists of data description, STATA analysis code, supplementary figures in PDF format, and the raw data archive, which is restricted access. |
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