Genomic epidemiological analysis of SARS-CoV-2 household transmission

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Title: Genomic epidemiological analysis of SARS-CoV-2 household transmission
Authors: Hare, DanielGonzalez, GabrielDean, JonathanMcDonnell, KathleenCarr, Michael J.De Gascun, Cillian
Permanent link: http://hdl.handle.net/10197/12347
Date: 19-Jul-2021
Online since: 2021-07-23T15:59:19Z
Abstract: Family clusters have contributed significantly to the onward spread of SARS-CoV-2. However, the dynamics of viral transmission in this setting remain incompletely understood. We describe the clinical and viral-phylogenetic characteristics of a family cluster of SARS-CoV-2 infections with a high attack rate, and explore how whole-genome sequencing (WGS) can inform outbreak investigations in this context. In this cluster, the first symptomatic case was a 22-month-old infant who developed rhinorrhoea and sneezing 2 days prior to attending a family gathering. Subsequently, seven family members in attendance at this event were diagnosed with SARS-CoV-2 infections, including the infant described. WGS revealed indistinguishable SARS-CoV-2 genomes recovered from the adults at the gathering, which were closely related genetically to B.1 lineage viruses circulating in the local community. However, a divergent viral sub-lineage was recovered from the infant and another child, each harbouring a distinguishing spike substitution (N30S). This suggested that the infant was unlikely to be the primary case, despite displaying symptoms first, and additional analysis of her nasopharyngeal swab revealed a picornavirus co-infection to account for her early symptoms. Our findings demonstrate how WGS can elucidate the transmission dynamics of SARS-CoV-2 infections within household clusters and provide useful information to support outbreak investigations. Additionally, our description of SARS-CoV-2 viral lineages and notable variants circulating in Ireland to date provides an important genomic-epidemiological baseline in the context of vaccine introduction.
Type of material: Journal Article
Publisher: Microbiology Society
Journal: Access Microbiology
Volume: 3
Issue: 7
Copyright (published version): 2021 the Authors
Keywords: SARS-CoV-2COVID-19Whole genome sequencingHousehold transmissionGenomic epidemiologyOutbreakCoronavirus
DOI: 10.1099/acmi.0.000252
Language: en
Status of Item: Peer reviewed
This item is made available under a Creative Commons License: https://creativecommons.org/licenses/by/3.0/ie/
Appears in Collections:Medicine Research Collection
UCD National Virus Reference Laboratory Research Collection

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