Genomic characterization of an outbreak with single origin and extensive contact tracing

Sequencing of SARS-CoV2 genomes throughout the COVID-19 pandemic has generated a wealth of data, but only a few studies have explored SARS-CoV2 genomes across larger transmission networks of tens to hundreds of persons. Existing reports have revealed limited genomic variation even across large sample sizes. Here, we couple SARS-CoV-2 genomes 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 PCR positive. Among the 121 retrievable genomes, 81 were identical to the index strain, thereby demonstrating that genomics has limited value in supporting contact-tracing data. In the cases where mutations were discovered, five genetic clusters were identified. We observed a household secondary attack rate of 67%, with 92% of household members infected among households with secondary transmission, showing that SARS-CoV2 introduction into large families are likely to affect all household members.