Open AccessGenomic epidemiological analysis of SARS-CoV-2 household transmission
Author(s) -
Daniel Hare,
Gabriel González,
Jonathan Dean,
Kathleen McDonnell,
Michael J. Carr,
Cillian F. De Gascun
Publication year - 2021
Publication title -
access microbiology
Language(s) - English
Resource type - Journals
ISSN - 2516-8290
DOI - 10.1099/acmi.0.000252
Subject(s) - context (archaeology) , transmission (telecommunications) , outbreak , lineage (genetic) , biology , cluster (spacecraft) , virology , pandemic , picornavirus , molecular epidemiology , genetics , genome , medicine , disease , covid-19 , genotype , gene , infectious disease (medical specialty) , paleontology , pathology , computer science , electrical engineering , programming language , engineering
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.