Spatial and temporal origin of the third SARS-CoV-2 Outbreak in Taiwan

ABSTRACT

Since the first report of SARS-CoV-2 in December 2019, Taiwan had gone through three local outbreaks. Unlike the first two, the spatial and temporal origin of the third outbreak (April 20 to November 5, 2021) is still unclear. We sequenced and reconstructed the phylogeny of SARS-CoV-2 genomes and find that the third outbreak was caused by a single virus lineage (T-III), which carries four genetic fingerprints, including spike M1237I (S-M1237I), and three silent changes. The T-III is closest to sequences derived from Turkey on February 8, 2021. The estimated date of divergence from the most recent common ancestor (TMRCA) of T-III is March 23, 2021 (95% HPD February 24 - April 13, 2021), almost one month before the first three confirmed cases on April 20, 2021. The effective population size of the T-III showed approximately 20-fold increase after the onset of the outbreak and reached a plateau in early June. Consequently, the lineage leading to the third outbreak most likely originated from Europe, perhaps Turkey, in February 2021. In addition, the T-III could have circulated in Taiwan in mid-March 2021. The virus was unnoticed while spreading within the community.