Comprehensive contact tracing during an outbreak of alpha-variant SARS-CoV-2 in a rural community reveals less viral genomic diversity and higher household secondary attack rates than expected

Abstract

Sequencing of SARS-CoV-2 genomes throughout the COVID-19 pandemic has generated a wealth of data on viral evolution across populations, but only a few studies have so far explored SARS-CoV-2 evolution across transmission networks of tens to hundreds of persons. Here, we couple data from SARS-CoV-2 sequencing with contact tracing data from an outbreak with a single origin in a rural Norwegian community where samples from all exposed persons were collected prospectively. A total of 134 nasopharyngeal samples were positive by PCR. Among the 121 retrievable genomes, 81 were identical to the genome of the introductor, thus demonstrating that genomics offers limited additional value to manual contact-tracing. In the cases where mutations were discovered, five small genetic clusters were identified. We observed a household secondary attack rate of 67%, with 92% of household members infected among households with secondary transmission, suggesting that SARS-CoV-2 introduction into large families are likely to affect all household members. ImportanceIn outbreak investigations, obtaining a full overview of infected individuals within a population is seldom acheived. We here present an example of just that, where a single introduction of B1.1.7 SARS-CoV-2 within a rural community allowed for tracing of the virus, from an introductor via dissemination through larger gatherings, into households. The outbreak occurred before widespread vaccination, allowing for a "natural" outbreak development with community lock-down. We show through sequencing that the virus can infect up to five consecutive persons without gaining mutations, thereby showing that contact tracing seems more important than sequencing for local outbreak investigations. We also show how families with small children are less likely to contain spread to all family members if SARS-CoV-2 enters the household either by a child or a caregiver, as isolation of the primary infected is difficult in such scenarios.