Investigation of One Familial Cluster of COVID-19 in Taiwan: Differentiation of Genetic Variation Among Isolates and Implications for Epidemiological Investigation and Surveillance by Genomic Assay

The COVID-19 pandemic has caused a global public health crisis. Taiwan experienced two waves of imported cases of coronavirus disease 2019 (COVID-19), first from China in January to late February, 2020 then from other countries starting in early March. As of Dec 14, 2020, 733 cases have been reported in Taiwan, with cases of entire families being infected. This study aimed to investigate the clinical characteristics and differentiation of genetic variation among isolates from a cluster of familial COVID-19 infection. The parents had pneumonia (Case 14, father, and Case 15, mother), the elder son (Case 17) had mild cough, and the younger son (Case 18) was asymptomatic. In this study, four full viral genomes were sequenced by Illumina sequencing directly from specimens. Phylogenetic tree analysis revealed that these sequences came from Italy, not China, indicating that no major strain has been circulating in Taiwan. Several novel mutations were observed in the asymptomatic patient, such as nsp2, nsp12, and nsp14. These mutations may be associated with the severity of COVID-19 infection.